Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xbb Working: n-1-20.cluster.ucsf.bkslab.org:/scratch/xiaobo/369383/xbb-8058088.28 Result: /scratch/xiaobo/369383/xbb-8058088.28 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbb 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/xbb mkdir: created directory `/scratch/xiaobo/369383' mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28' /scratch/xiaobo/369383/xbb-8058088.28 /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/369383/xbb-8058088.28/working' mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/protonate' Storing results in /scratch/xiaobo/369383/xbb-8058088.28/finished Working in /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 /scratch/xiaobo/369383/xbb-8058088.28/working/protonate /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Using inputs as protomers/tautomers. No processing done 469 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/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Bulk generating 3D conformations all protomers in /scratch/xiaobo/369383/xbb-8058088.28/working/3D mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/369383/xbb-8058088.28/working/protonate/xbb-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 ZINC001611685853 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building' mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001611685853 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/1 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/1' -> `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)NC1CC2(C1)COC(C)(C)C2) `ZINC001611685853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611685853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611685853 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 14, 14, 14, 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, 56, 57]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/2 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/2' -> `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)NC1CC2(C1)COC(C)(C)C2) `ZINC001611685853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611685853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611685853 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 11, 14, 14, 14, 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, 56, 57]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/3 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/3' -> `2.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)NC1CC2(C1)COC(C)(C)C2) `ZINC001611685853.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001611685853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611685853 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 14, 14, 14, 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, 56, 57]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001611685853 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/finished' Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 Building ZINC001611685853 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001611685853 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 1) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2) `ZINC001611685853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611685853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611685853 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 14, 14, 14, 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, 56, 57]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 2) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2) `ZINC001611685853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611685853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611685853 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 11, 14, 14, 14, 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, 56, 57]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 3) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2) `ZINC001611685853.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001611685853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611685853 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 14, 14, 14, 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, 56, 57]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001611685853 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 Building ZINC001611685853 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001611685853 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 1) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2) `ZINC001611685853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001611685853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611685853 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 14, 14, 14, 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, 56, 57]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 2) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2) `ZINC001611685853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001611685853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611685853 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 11, 14, 14, 14, 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, 56, 57]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 3) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2) `ZINC001611685853.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001611685853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001611685853 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CC2(C1)COC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 14, 14, 14, 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, 56, 57]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001611685853 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001611685853 Building ZINC001614715569 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001614715569 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/4 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001614715569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001614715569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001614715569 none COC(=O)c1sc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 21, 42, 21, 21, 21, 21, 21, 21, 21, 21, 13, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 42, 42, 42, 21, 21, 21, 21, 13, 13, 3, 5, 5] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/5 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001614715569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001614715569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001614715569 none COC(=O)c1sc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 21, 42, 21, 21, 21, 21, 21, 21, 21, 21, 13, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 42, 42, 42, 21, 21, 21, 21, 13, 13, 3, 5, 5] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001614715569 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 Building ZINC001614715569 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001614715569 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 4) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)c1sc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001614715569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001614715569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001614715569 none COC(=O)c1sc2ccccc2c1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 21, 42, 21, 21, 21, 21, 21, 21, 21, 21, 13, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 42, 42, 42, 21, 21, 21, 21, 13, 13, 3, 5, 5] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 5) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)c1sc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001614715569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001614715569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001614715569 none COC(=O)c1sc2ccccc2c1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 21, 42, 21, 21, 21, 21, 21, 21, 21, 21, 13, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 42, 42, 42, 21, 21, 21, 21, 13, 13, 3, 5, 5] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001614715569 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614715569 Building ZINC001614906215 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001614906215 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/6 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(OCCSc2ccc(Cl)cc2)cc1) `ZINC001614906215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001614906215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001614906215 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(OCCSc2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 11, 11, 6, 9, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 44, 44, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 11, 35, 33, 29, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/7 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(OCCSc2ccc(Cl)cc2)cc1) `ZINC001614906215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001614906215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001614906215 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(OCCSc2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 11, 11, 6, 11, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 44, 44, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 11, 35, 33, 29, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001614906215 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 Building ZINC001614906215 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001614906215 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 6) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(OCCSc2ccc(Cl)cc2)cc1) `ZINC001614906215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001614906215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001614906215 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(OCCSc2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 11, 11, 6, 9, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 44, 44, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 11, 35, 33, 29, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 7) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(OCCSc2ccc(Cl)cc2)cc1) `ZINC001614906215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001614906215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001614906215 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(OCCSc2ccc(Cl)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 11, 11, 6, 11, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 44, 44, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 7, 34, 11, 35, 33, 29, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001614906215 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001614906215 Building ZINC001616147244 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616147244 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/8 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCCCOc3ccccc3)c(Cl)c2)cn1) `ZINC001616147244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616147244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001616147244 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCCCOc3ccccc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 15, 19, 25, 26, 34, 34, 34, 34, 34, 34, 4, 4, 4, 3, 3, 6, 6, 6, 6, 6, 3, 2, 4, 4, 19, 19, 25, 25, 26, 26, 34, 34, 34, 34, 34, 4, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/9 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCCCOc3ccccc3)c(Cl)c2)cn1) `ZINC001616147244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616147244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001616147244 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCCCOc3ccccc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 4, 4, 15, 20, 30, 33, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 2, 4, 4, 20, 20, 30, 30, 33, 33, 42, 42, 42, 42, 42, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616147244 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 Building ZINC001616147244 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616147244 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 8) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCCCOc3ccccc3)c(Cl)c2)cn1) `ZINC001616147244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616147244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001616147244 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCCCOc3ccccc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 15, 19, 25, 26, 34, 34, 34, 34, 34, 34, 4, 4, 4, 3, 3, 6, 6, 6, 6, 6, 3, 2, 4, 4, 19, 19, 25, 25, 26, 26, 34, 34, 34, 34, 34, 4, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 9) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCCCOc3ccccc3)c(Cl)c2)cn1) `ZINC001616147244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616147244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001616147244 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCCCOc3ccccc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 4, 4, 15, 20, 30, 33, 42, 42, 42, 42, 42, 42, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 2, 4, 4, 20, 20, 30, 30, 33, 33, 42, 42, 42, 42, 42, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616147244 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616147244 Building ZINC001616329391 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616329391 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/10 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/10' -> `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](C1CC1)C1CCOCC1) `ZINC001616329391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616329391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616329391 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C1CC1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 6, 6, 6, 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, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/11 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/11' -> `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](C1CC1)C1CCOCC1) `ZINC001616329391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616329391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616329391 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C1CC1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 8, 6, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 8, 8, 8, 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, 57]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616329391 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 Building ZINC001616329391 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616329391 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 10) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C1CC1)C1CCOCC1) `ZINC001616329391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616329391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616329391 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C1CC1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 6, 6, 6, 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, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 11) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C1CC1)C1CCOCC1) `ZINC001616329391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616329391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616329391 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C1CC1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 8, 6, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 8, 8, 8, 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, 57]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616329391 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329391 Building ZINC001616329392 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616329392 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/12 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/12' -> `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](C1CC1)C1CCOCC1) `ZINC001616329392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616329392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616329392 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C1CC1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 9, 9, 7, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 9, 9, 9, 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, 57]) total number of confs: 76 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/13 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/13' -> `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](C1CC1)C1CCOCC1) `ZINC001616329392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616329392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616329392 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C1CC1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 10, 10, 9, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 10, 10, 10, 10, 10, 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, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616329392 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 Building ZINC001616329392 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616329392 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 12) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C1CC1)C1CCOCC1) `ZINC001616329392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616329392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616329392 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C1CC1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 9, 9, 7, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 9, 9, 9, 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, 57]) total number of confs: 76 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 13) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C1CC1)C1CCOCC1) `ZINC001616329392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616329392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001616329392 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C1CC1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 10, 10, 9, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 10, 10, 10, 10, 10, 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, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616329392 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616329392 Building ZINC001616349910 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616349910 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/14 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(I)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616349910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616349910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001616349910 none O=C(Nc1ccc(I)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 16, 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, 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: [5, 1, 5, 5, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 12, 12, 12, 12, 12, 5, 30, 30, 30, 12, 12] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/15 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(I)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616349910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616349910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001616349910 none O=C(Nc1ccc(I)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 16, 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, 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: [5, 1, 5, 5, 30, 30, 20, 30, 30, 30, 30, 1, 1, 1, 12, 12, 12, 12, 12, 5, 30, 30, 30, 12, 12] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616349910 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 Building ZINC001616349910 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616349910 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 14) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(I)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616349910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616349910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001616349910 none O=C(Nc1ccc(I)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 16, 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, 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: [5, 1, 5, 5, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 12, 12, 12, 12, 12, 5, 30, 30, 30, 12, 12] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 15) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(I)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001616349910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616349910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 28 natoms 27 natoms 26 natoms 25 names: ZINC001616349910 none O=C(Nc1ccc(I)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 16, 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, 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: [5, 1, 5, 5, 30, 30, 20, 30, 30, 30, 30, 1, 1, 1, 12, 12, 12, 12, 12, 5, 30, 30, 30, 12, 12] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616349910 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616349910 Building ZINC001616407046 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616407046 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/16 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCN1C(=O)OC(C)(C)C) `ZINC001616407046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616407046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001616407046 none CC(C)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 20, 11, 11, 11, 6, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 29, 29, 47, 47, 47, 47, 20, 20, 20, 20, 20, 20, 20, 11, 11, 3, 1, 3, 11, 11, 11, 11, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/17 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCN1C(=O)OC(C)(C)C) `ZINC001616407046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616407046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001616407046 none CC(C)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 19, 11, 11, 11, 6, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 29, 29, 48, 48, 48, 48, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 1, 3, 11, 11, 11, 11, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616407046 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 Building ZINC001616407046 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616407046 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 16) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCN1C(=O)OC(C)(C)C) `ZINC001616407046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616407046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001616407046 none CC(C)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 20, 11, 11, 11, 6, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 29, 29, 47, 47, 47, 47, 20, 20, 20, 20, 20, 20, 20, 11, 11, 3, 1, 3, 11, 11, 11, 11, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 17) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCN1C(=O)OC(C)(C)C) `ZINC001616407046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616407046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001616407046 none CC(C)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CCN1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 19, 11, 11, 11, 6, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 11, 11, 29, 29, 48, 48, 48, 48, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 1, 3, 11, 11, 11, 11, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616407046 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616407046 Building ZINC001616430247 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616430247 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/18 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc(c3ccccc3Br)no2)c1) `ZINC001616430247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616430247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616430247 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc(c3ccccc3Br)no2)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', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.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, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 21, 21, 21, 28, 28, 21, 28, 28, 28, 21, 21, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 28, 28, 28, 28, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/19 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc(c3ccccc3Br)no2)c1) `ZINC001616430247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616430247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616430247 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc(c3ccccc3Br)no2)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', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.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, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 34, 34, 34, 34, 34, 34, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616430247 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 Building ZINC001616430247 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616430247 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 18) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc(c3ccccc3Br)no2)c1) `ZINC001616430247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616430247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616430247 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc(c3ccccc3Br)no2)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', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.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, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 21, 21, 21, 28, 28, 21, 28, 28, 28, 21, 21, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 28, 28, 28, 28, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 19) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc(c3ccccc3Br)no2)c1) `ZINC001616430247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616430247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616430247 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2nc(c3ccccc3Br)no2)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', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.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, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 34, 34, 34, 34, 34, 34, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616430247 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430247 Building ZINC001616430249 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616430249 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/20 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc(c3ccccc3Br)no2)c1) `ZINC001616430249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616430249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616430249 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc(c3ccccc3Br)no2)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', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.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, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 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, 3, 3, 3, 3, 3, 3, 14, 14, 14, 33, 33, 21, 33, 33, 33, 14, 14, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3, 3, 3, 33, 33, 30, 33, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/21 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc(c3ccccc3Br)no2)c1) `ZINC001616430249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616430249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616430249 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc(c3ccccc3Br)no2)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', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.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, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 20, 20, 20, 26, 26, 21, 26, 26, 26, 20, 20, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 26, 26, 25, 26, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616430249 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 Building ZINC001616430249 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616430249 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 20) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc(c3ccccc3Br)no2)c1) `ZINC001616430249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616430249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616430249 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc(c3ccccc3Br)no2)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', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.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, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 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, 3, 3, 3, 3, 3, 3, 14, 14, 14, 33, 33, 21, 33, 33, 33, 14, 14, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3, 3, 3, 33, 33, 30, 33, 3] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 21) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc(c3ccccc3Br)no2)c1) `ZINC001616430249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616430249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616430249 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2nc(c3ccccc3Br)no2)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', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.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, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 20, 20, 20, 26, 26, 21, 26, 26, 26, 20, 20, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 26, 26, 25, 26, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616430249 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616430249 Building ZINC001616468430 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616468430 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/22 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCCC1) `ZINC001616468430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616468430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001616468430 none CC(C)(C)OC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 18, 37, 10, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/23 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCCC1) `ZINC001616468430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616468430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001616468430 none CC(C)(C)OC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 20, 39, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 5, 5, 24, 24, 24, 24, 24, 24, 24, 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, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616468430 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 Building ZINC001616468430 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616468430 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 22) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCCC1) `ZINC001616468430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616468430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001616468430 none CC(C)(C)OC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 18, 37, 10, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 23) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCCC1) `ZINC001616468430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616468430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001616468430 none CC(C)(C)OC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 20, 39, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 5, 5, 24, 24, 24, 24, 24, 24, 24, 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, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616468430 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616468430 Building ZINC001616734892 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616734892 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/24 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C) `ZINC001616734892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616734892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001616734892 none CN(CC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 4, 29, 46, 46, 50, 50, 50, 50, 29, 29, 29, 17, 17, 4, 4, 4, 4, 4, 2, 1, 2, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/25 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C) `ZINC001616734892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616734892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001616734892 none CN(CC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 28, 47, 47, 50, 50, 50, 50, 28, 28, 28, 16, 16, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616734892 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 Building ZINC001616734892 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616734892 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 24) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C) `ZINC001616734892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616734892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001616734892 none CN(CC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 4, 29, 46, 46, 50, 50, 50, 50, 29, 29, 29, 17, 17, 4, 4, 4, 4, 4, 2, 1, 2, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 25) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C) `ZINC001616734892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616734892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001616734892 none CN(CC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 16, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 28, 47, 47, 50, 50, 50, 50, 28, 28, 28, 16, 16, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 7, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616734892 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616734892 Building ZINC001616831918 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616831918 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/26 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CSCc3ccc(Br)cc32)cc1Cl) `ZINC001616831918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616831918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616831918 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CSCc3ccc(Br)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', 'H', 'C.3', 'S.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 3, 15, 15, 15, 15, 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/27 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CSCc3ccc(Br)cc32)cc1Cl) `ZINC001616831918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616831918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616831918 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CSCc3ccc(Br)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', 'H', 'C.3', 'S.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 3, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616831918 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 Building ZINC001616831918 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616831918 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 26) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CSCc3ccc(Br)cc32)cc1Cl) `ZINC001616831918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616831918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616831918 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CSCc3ccc(Br)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', 'H', 'C.3', 'S.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 3, 15, 15, 15, 15, 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 27) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CSCc3ccc(Br)cc32)cc1Cl) `ZINC001616831918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616831918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616831918 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CSCc3ccc(Br)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', 'H', 'C.3', 'S.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 3, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616831918 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831918 Building ZINC001616831919 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616831919 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/28 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CSCc3ccc(Br)cc32)cc1Cl) `ZINC001616831919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616831919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616831919 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CSCc3ccc(Br)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', 'H', 'C.3', 'S.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 3, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/29 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CSCc3ccc(Br)cc32)cc1Cl) `ZINC001616831919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616831919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616831919 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CSCc3ccc(Br)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', 'H', 'C.3', 'S.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 3, 15, 15, 15, 15, 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616831919 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 Building ZINC001616831919 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616831919 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 28) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CSCc3ccc(Br)cc32)cc1Cl) `ZINC001616831919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616831919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616831919 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CSCc3ccc(Br)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', 'H', 'C.3', 'S.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 3, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 29) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CSCc3ccc(Br)cc32)cc1Cl) `ZINC001616831919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616831919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001616831919 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CSCc3ccc(Br)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', 'H', 'C.3', 'S.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 3, 15, 15, 15, 15, 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, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616831919 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616831919 Building ZINC001616946036 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616946036 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/30 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001616946036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616946036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616946036 none CC(=O)c1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 10, 10, 3, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 22, 22, 22, 10, 10, 10, 3, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/31 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001616946036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616946036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616946036 none CC(=O)c1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 10, 10, 2, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 24, 24, 24, 10, 10, 10, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616946036 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 Building ZINC001616946036 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001616946036 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 30) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(=O)c1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001616946036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001616946036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616946036 none CC(=O)c1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 10, 10, 3, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 22, 22, 22, 10, 10, 10, 3, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 31) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(=O)c1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001616946036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001616946036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001616946036 none CC(=O)c1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7] 0 hydrogens 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, 10, 24, 10, 10, 2, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 24, 24, 24, 10, 10, 10, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001616946036 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001616946036 Building ZINC001617023458 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617023458 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/32 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617023458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617023458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001617023458 none O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[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.ar', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 9, 6, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 6, 9, 9, 9, 29, 29, 29, 29, 29, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/33 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617023458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617023458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001617023458 none O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[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.ar', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617023458 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 Building ZINC001617023458 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617023458 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 32) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617023458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617023458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001617023458 none O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[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.ar', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 9, 6, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 6, 9, 9, 9, 29, 29, 29, 29, 29, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 33) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617023458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617023458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001617023458 none O=C(Nc1ccccc1CS(=O)(=O)c1ccccc1)[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.ar', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617023458 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617023458 Building ZINC001617107996 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617107996 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/34 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2cc(Br)c(F)cc2[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617107996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617107996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001617107996 none O=C(Nc1nc2cc(Br)c(F)cc2[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 17, 1, 15, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 22 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]) total number of confs: 34 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/35 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2cc(Br)c(F)cc2[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617107996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617107996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001617107996 none O=C(Nc1nc2cc(Br)c(F)cc2[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 17, 1, 15, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 22 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]) total number of confs: 34 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617107996 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 Building ZINC001617107996 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617107996 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 34) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(Nc1nc2cc(Br)c(F)cc2[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617107996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617107996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001617107996 none O=C(Nc1nc2cc(Br)c(F)cc2[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 17, 1, 15, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 22 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]) total number of confs: 34 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 35) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(Nc1nc2cc(Br)c(F)cc2[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617107996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617107996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001617107996 none O=C(Nc1nc2cc(Br)c(F)cc2[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 17, 1, 15, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 22 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]) total number of confs: 34 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617107996 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617107996 Building ZINC001617120619 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617120619 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/36 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/36' -> `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(Cl)c(NC(=O)C2CC2)c1) `ZINC001617120619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617120619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617120619 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(NC(=O)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 12, 12, 12, 12, 12, 12, 23, 23, 23, 36, 36, 12, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 12, 12, 23, 36, 36, 36, 36, 36, 12] 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: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/37 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/37' -> `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(Cl)c(NC(=O)C2CC2)c1) `ZINC001617120619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617120619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617120619 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(NC(=O)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 23, 23, 23, 36, 36, 11, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 11, 11, 23, 36, 36, 36, 36, 36, 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]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617120619 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 Building ZINC001617120619 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617120619 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 36) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(NC(=O)C2CC2)c1) `ZINC001617120619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617120619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617120619 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(NC(=O)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 12, 12, 12, 12, 12, 12, 23, 23, 23, 36, 36, 12, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 12, 12, 23, 36, 36, 36, 36, 36, 12] 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: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 37) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(NC(=O)C2CC2)c1) `ZINC001617120619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617120619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617120619 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)c(NC(=O)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 23, 23, 23, 36, 36, 11, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 11, 11, 23, 36, 36, 36, 36, 36, 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]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617120619 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617120619 Building ZINC001617129622 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617129622 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/38 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 16, 16, 16, 16, 27, 29, 29, 27, 29, 29, 29, 29, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 27, 27, 29, 29, 29, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/39 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 16, 16, 16, 16, 27, 29, 29, 27, 29, 29, 29, 29, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 27, 27, 29, 29, 29, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/40 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/40' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 18, 18, 18, 18, 31, 33, 33, 31, 33, 33, 33, 33, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 31, 31, 33, 33, 33, 18, 18, 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/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/41 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/41' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 18, 18, 18, 18, 31, 33, 33, 31, 33, 33, 33, 33, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 31, 31, 33, 33, 33, 18, 18, 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/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617129622 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 Building ZINC001617129622 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617129622 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 38) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 16, 16, 16, 16, 27, 29, 29, 27, 29, 29, 29, 29, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 27, 27, 29, 29, 29, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 39) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 16, 16, 16, 16, 27, 29, 29, 27, 29, 29, 29, 29, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 27, 27, 29, 29, 29, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 40) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 18, 18, 18, 18, 31, 33, 33, 31, 33, 33, 33, 33, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 31, 31, 33, 33, 33, 18, 18, 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/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 41) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 18, 18, 18, 18, 31, 33, 33, 31, 33, 33, 33, 33, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 31, 31, 33, 33, 33, 18, 18, 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/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617129622 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 Building ZINC001617129622 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617129622 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 38) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 16, 16, 16, 16, 27, 29, 29, 27, 29, 29, 29, 29, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 27, 27, 29, 29, 29, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 39) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 16, 16, 16, 16, 27, 29, 29, 27, 29, 29, 29, 29, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 27, 27, 29, 29, 29, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 40) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 18, 18, 18, 18, 31, 33, 33, 31, 33, 33, 33, 33, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 31, 31, 33, 33, 33, 18, 18, 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/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 41) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 18, 18, 18, 18, 31, 33, 33, 31, 33, 33, 33, 33, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 31, 31, 33, 33, 33, 18, 18, 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/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617129622 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 Building ZINC001617129622 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617129622 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 38) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 16, 16, 16, 16, 27, 29, 29, 27, 29, 29, 29, 29, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 27, 27, 29, 29, 29, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 39) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 16, 16, 16, 16, 27, 29, 29, 27, 29, 29, 29, 29, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 27, 27, 29, 29, 29, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 40) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 18, 18, 18, 18, 31, 33, 33, 31, 33, 33, 33, 33, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 31, 31, 33, 33, 33, 18, 18, 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/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 41) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129622.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617129622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129622 none O=C(N[C@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 18, 18, 18, 18, 31, 33, 33, 31, 33, 33, 33, 33, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 31, 31, 33, 33, 33, 18, 18, 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/369383/xbb-8058088.28/working/building/ZINC001617129622 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617129622 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129622 Building ZINC001617129625 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617129625 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/42 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 20, 20, 20, 20, 20, 20, 32, 33, 33, 33, 33, 33, 33, 33, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 20, 20, 20, 20, 32, 32, 33, 33, 33, 20, 20, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/43 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 20, 20, 20, 20, 20, 20, 32, 33, 33, 33, 33, 33, 33, 33, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 20, 20, 20, 20, 32, 32, 33, 33, 33, 20, 20, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/44 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/44' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 17, 17, 17, 17, 17, 17, 28, 29, 29, 29, 29, 29, 29, 29, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 17, 17, 17, 17, 28, 28, 29, 29, 29, 17, 17, 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/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/45 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/45' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 17, 17, 17, 17, 17, 17, 28, 29, 29, 29, 29, 29, 29, 29, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 17, 17, 17, 17, 28, 28, 29, 29, 29, 17, 17, 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/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617129625 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 Building ZINC001617129625 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617129625 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 42) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 20, 20, 20, 20, 20, 20, 32, 33, 33, 33, 33, 33, 33, 33, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 20, 20, 20, 20, 32, 32, 33, 33, 33, 20, 20, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 43) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 20, 20, 20, 20, 20, 20, 32, 33, 33, 33, 33, 33, 33, 33, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 20, 20, 20, 20, 32, 32, 33, 33, 33, 20, 20, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 44) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 17, 17, 17, 17, 17, 17, 28, 29, 29, 29, 29, 29, 29, 29, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 17, 17, 17, 17, 28, 28, 29, 29, 29, 17, 17, 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/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 45) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 17, 17, 17, 17, 17, 17, 28, 29, 29, 29, 29, 29, 29, 29, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 17, 17, 17, 17, 28, 28, 29, 29, 29, 17, 17, 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/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617129625 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 Building ZINC001617129625 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617129625 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 42) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 20, 20, 20, 20, 20, 20, 32, 33, 33, 33, 33, 33, 33, 33, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 20, 20, 20, 20, 32, 32, 33, 33, 33, 20, 20, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 43) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 20, 20, 20, 20, 20, 20, 32, 33, 33, 33, 33, 33, 33, 33, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 20, 20, 20, 20, 32, 32, 33, 33, 33, 20, 20, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 44) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 17, 17, 17, 17, 17, 17, 28, 29, 29, 29, 29, 29, 29, 29, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 17, 17, 17, 17, 28, 28, 29, 29, 29, 17, 17, 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/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 45) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 17, 17, 17, 17, 17, 17, 28, 29, 29, 29, 29, 29, 29, 29, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 17, 17, 17, 17, 28, 28, 29, 29, 29, 17, 17, 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/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617129625 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 Building ZINC001617129625 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617129625 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 42) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 20, 20, 20, 20, 20, 20, 32, 33, 33, 33, 33, 33, 33, 33, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 20, 20, 20, 20, 32, 32, 33, 33, 33, 20, 20, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 43) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 20, 20, 20, 20, 20, 20, 32, 33, 33, 33, 33, 33, 33, 33, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 20, 20, 20, 20, 32, 32, 33, 33, 33, 20, 20, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 44) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 17, 17, 17, 17, 17, 17, 28, 29, 29, 29, 29, 29, 29, 29, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 17, 17, 17, 17, 28, 28, 29, 29, 29, 17, 17, 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/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 45) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001617129625.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617129625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001617129625 none O=C(N[C@@H]1CCCN(Cc2ccc(F)cc2Cl)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 17, 17, 17, 17, 17, 17, 28, 29, 29, 29, 29, 29, 29, 29, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 17, 17, 17, 17, 28, 28, 29, 29, 29, 17, 17, 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/369383/xbb-8058088.28/working/building/ZINC001617129625 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617129625 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617129625 Building ZINC001617133943 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617133943 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/46 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)c1) `ZINC001617133943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617133943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617133943 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 4, 5, 5, 5, 5, 5, 13, 23, 28, 28, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 2, 4, 4, 5, 5, 13, 13, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/47 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)c1) `ZINC001617133943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617133943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617133943 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 4, 4, 4, 4, 4, 4, 9, 25, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 25, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/369383/xbb-8058088.28/working/building/ZINC001617133943 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617133943 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943 Building ZINC001617133943 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617133943 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 46) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)c1) `ZINC001617133943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617133943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617133943 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 4, 5, 5, 5, 5, 5, 13, 23, 28, 28, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 2, 4, 4, 5, 5, 13, 13, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 47) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)c1) `ZINC001617133943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617133943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617133943 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 4, 4, 4, 4, 4, 4, 9, 25, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 25, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/369383/xbb-8058088.28/working/building/ZINC001617133943 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617133943 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133943 Building ZINC001617133946 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617133946 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/48 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)c1) `ZINC001617133946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617133946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617133946 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 4, 4, 4, 4, 4, 4, 9, 23, 29, 29, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/49 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)c1) `ZINC001617133946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617133946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617133946 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 4, 4, 4, 4, 4, 13, 22, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 13, 13, 22, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 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/369383/xbb-8058088.28/working/building/ZINC001617133946 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617133946 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946 Building ZINC001617133946 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617133946 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 48) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)c1) `ZINC001617133946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617133946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617133946 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 4, 4, 4, 4, 4, 4, 9, 23, 29, 29, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 2] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 49) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)c1) `ZINC001617133946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617133946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617133946 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CNC(=O)OC(C)(C)C)Cc3cc(F)ccc32)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 15, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 4, 4, 4, 4, 4, 13, 22, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 13, 13, 22, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 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/369383/xbb-8058088.28/working/building/ZINC001617133946 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617133946 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617133946 Building ZINC001617135491 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617135491 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/50 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 21, 21, 21, 21, 21, 21, 21, 21, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 38, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/51 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 21, 21, 21, 21, 21, 21, 21, 21, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 38, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/52 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/52' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 20, 20, 20, 20, 20, 20, 20, 20, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 3, 20, 20, 20, 20, 20, 20, 36, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/53 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/53' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 20, 20, 20, 20, 20, 20, 20, 20, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 3, 20, 20, 20, 20, 20, 20, 36, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617135491 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 Building ZINC001617135491 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617135491 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 50) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 21, 21, 21, 21, 21, 21, 21, 21, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 38, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 51) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 21, 21, 21, 21, 21, 21, 21, 21, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 38, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 52) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 20, 20, 20, 20, 20, 20, 20, 20, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 3, 20, 20, 20, 20, 20, 20, 36, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 53) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 20, 20, 20, 20, 20, 20, 20, 20, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 3, 20, 20, 20, 20, 20, 20, 36, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617135491 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 Building ZINC001617135491 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617135491 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 50) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 21, 21, 21, 21, 21, 21, 21, 21, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 38, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 51) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 21, 21, 21, 21, 21, 21, 21, 21, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 38, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 52) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 20, 20, 20, 20, 20, 20, 20, 20, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 3, 20, 20, 20, 20, 20, 20, 36, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 53) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 20, 20, 20, 20, 20, 20, 20, 20, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 3, 20, 20, 20, 20, 20, 20, 36, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617135491 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 Building ZINC001617135491 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617135491 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 50) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 21, 21, 21, 21, 21, 21, 21, 21, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 38, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 51) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 21, 21, 21, 21, 21, 21, 21, 21, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 3, 21, 21, 21, 21, 21, 21, 38, 38, 43, 43, 38, 43, 43, 21, 21, 21, 21, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 52) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 20, 20, 20, 20, 20, 20, 20, 20, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 3, 20, 20, 20, 20, 20, 20, 36, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 53) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135491.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617135491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135491 none O=C(N[C@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 20, 20, 20, 20, 20, 20, 20, 20, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 3, 20, 20, 20, 20, 20, 20, 36, 36, 43, 43, 36, 43, 43, 20, 20, 20, 20, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617135491 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135491 Building ZINC001617135493 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617135493 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/54 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 17, 17, 17, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 2, 17, 17, 17, 17, 17, 17, 34, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/55 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 17, 17, 17, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 2, 17, 17, 17, 17, 17, 17, 34, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/56 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/56' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 16, 33, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/57 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/57' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 16, 33, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617135493 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 Building ZINC001617135493 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617135493 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 54) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 17, 17, 17, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 2, 17, 17, 17, 17, 17, 17, 34, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 55) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 17, 17, 17, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 2, 17, 17, 17, 17, 17, 17, 34, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 56) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 16, 33, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 57) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 16, 33, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617135493 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 Building ZINC001617135493 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617135493 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 54) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 17, 17, 17, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 2, 17, 17, 17, 17, 17, 17, 34, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 55) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 17, 17, 17, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 2, 17, 17, 17, 17, 17, 17, 34, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 56) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 16, 33, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 57) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 16, 33, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617135493 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 Building ZINC001617135493 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001617135493 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 54) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 17, 17, 17, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 2, 17, 17, 17, 17, 17, 17, 34, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 55) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 17, 17, 17, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 2, 17, 17, 17, 17, 17, 17, 34, 34, 42, 42, 34, 42, 42, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 56) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 16, 33, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 57) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001617135493.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001617135493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617135493 none O=C(N[C@@H]1CC[C@@H]2CN(Cc3ccccc3)C[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 16, 16, 16, 16, 33, 33, 40, 40, 33, 40, 40, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617135493 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135493 Building ZINC001617135648 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617135648 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/58 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001617135648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617135648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001617135648 none COc1ccc(CN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [26, 26, 18, 26, 26, 15, 7, 3, 7, 12, 12, 12, 12, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 15, 15, 12, 12, 6, 6, 26, 26] 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]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/59 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001617135648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617135648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001617135648 none COc1ccc(CN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [28, 26, 17, 28, 28, 17, 9, 4, 9, 14, 14, 14, 14, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 17, 17, 14, 14, 7, 7, 28, 28] 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617135648 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 Building ZINC001617135648 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617135648 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 58) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001617135648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617135648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001617135648 none COc1ccc(CN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [26, 26, 18, 26, 26, 15, 7, 3, 7, 12, 12, 12, 12, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 15, 15, 12, 12, 6, 6, 26, 26] 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]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 59) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001617135648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617135648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001617135648 none COc1ccc(CN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [28, 26, 17, 28, 28, 17, 9, 4, 9, 14, 14, 14, 14, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 17, 17, 14, 14, 7, 7, 28, 28] 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617135648 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617135648 Building ZINC001617416077 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617416077 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/60 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001617416077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617416077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617416077 none CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 35, 43, 35, 35, 35, 35, 5, 35, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 35, 35, 35, 35, 35, 35, 5, 5, 3, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/61 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001617416077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617416077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617416077 none CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 36, 44, 36, 36, 36, 36, 7, 36, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 5, 5, 3, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617416077 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 Building ZINC001617416077 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617416077 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 60) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001617416077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617416077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617416077 none CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 35, 43, 35, 35, 35, 35, 5, 35, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 35, 35, 35, 35, 35, 35, 5, 5, 3, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 61) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001617416077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617416077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617416077 none CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 36, 44, 36, 36, 36, 36, 7, 36, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 5, 5, 3, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617416077 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416077 Building ZINC001617416078 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617416078 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/62 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001617416078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617416078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617416078 none CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 36, 44, 36, 36, 36, 36, 7, 36, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 5, 5, 3, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/63 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001617416078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617416078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617416078 none CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 36, 44, 36, 36, 36, 36, 5, 36, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 5, 5, 3, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617416078 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 Building ZINC001617416078 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617416078 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 62) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001617416078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617416078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617416078 none CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 36, 44, 36, 36, 36, 36, 7, 36, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 5, 5, 3, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 63) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1) `ZINC001617416078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617416078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001617416078 none CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 36, 44, 36, 36, 36, 36, 5, 36, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 36, 36, 36, 36, 36, 36, 5, 5, 3, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617416078 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617416078 Building ZINC001617417302 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617417302 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/64 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001617417302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617417302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001617417302 none CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 50, 37, 37, 37, 37, 6, 37, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 5, 5, 3, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/65 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001617417302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617417302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001617417302 none CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 50, 39, 39, 39, 39, 6, 39, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 5, 5, 3, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617417302 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 Building ZINC001617417302 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617417302 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 64) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001617417302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617417302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001617417302 none CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 50, 37, 37, 37, 37, 6, 37, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 5, 5, 3, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 65) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001617417302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617417302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001617417302 none CC(C)(C)OC(=O)N1CCC[C@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 50, 39, 39, 39, 39, 6, 39, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39, 5, 5, 3, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617417302 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417302 Building ZINC001617417303 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617417303 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/66 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001617417303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617417303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001617417303 none CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 50, 40, 40, 40, 40, 6, 40, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 5, 5, 3, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/67 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001617417303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617417303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001617417303 none CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 38, 38, 38, 38, 6, 38, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 5, 5, 3, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617417303 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 Building ZINC001617417303 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617417303 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 66) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001617417303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617417303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001617417303 none CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 50, 40, 40, 40, 40, 6, 40, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 5, 5, 3, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 67) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001617417303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617417303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001617417303 none CC(C)(C)OC(=O)N1CCC[C@@H]1c1nccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1 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.ar', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 38, 38, 38, 38, 6, 38, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 5, 5, 3, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617417303 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617417303 Building ZINC001617428013 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617428013 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/68 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)c2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21) `ZINC001617428013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617428013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617428013 none COc1ccc(Br)c2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', '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, 17, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 17, 17, 17, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/69 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)c2sc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21) `ZINC001617428013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617428013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617428013 none COc1ccc(Br)c2sc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', '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, 17, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 10, 10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617428013 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 Building ZINC001617428013 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617428013 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 68) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(Br)c2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21) `ZINC001617428013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617428013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617428013 none COc1ccc(Br)c2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', '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, 17, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 17, 17, 17, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 69) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(Br)c2sc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21) `ZINC001617428013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617428013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001617428013 none COc1ccc(Br)c2sc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', '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, 17, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 10, 10, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617428013 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617428013 Building ZINC001617476205 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617476205 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/70 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001617476205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617476205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001617476205 none COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 9, 15, 15, 8, 8, 8, 8, 8, 8, 18, 18, 36, 37, 37, 37, 8, 8, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 15, 15, 15, 15, 8, 8, 37, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 59, 60, 61, 56, 58, 57, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/71 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001617476205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617476205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001617476205 none COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 13, 11, 13, 13, 9, 9, 9, 9, 9, 9, 20, 20, 39, 40, 40, 40, 9, 9, 9, 2, 9, 1, 1, 1, 3, 3, 1, 2, 3, 3, 16, 16, 16, 13, 13, 13, 13, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617476205 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 Building ZINC001617476205 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617476205 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 70) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001617476205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617476205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001617476205 none COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 15, 15, 15, 9, 15, 15, 8, 8, 8, 8, 8, 8, 18, 18, 36, 37, 37, 37, 8, 8, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 15, 15, 15, 15, 8, 8, 37, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 59, 60, 61, 56, 58, 57, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 71) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001617476205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617476205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001617476205 none COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 13, 13, 11, 13, 13, 9, 9, 9, 9, 9, 9, 20, 20, 39, 40, 40, 40, 9, 9, 9, 2, 9, 1, 1, 1, 3, 3, 1, 2, 3, 3, 16, 16, 16, 13, 13, 13, 13, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617476205 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476205 Building ZINC001617476206 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617476206 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/72 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001617476206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617476206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001617476206 none COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 11, 13, 13, 8, 8, 8, 8, 8, 8, 19, 19, 39, 40, 40, 40, 8, 8, 8, 2, 8, 1, 1, 1, 2, 2, 1, 2, 2, 2, 15, 15, 15, 13, 13, 13, 13, 8, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/73 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001617476206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617476206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001617476206 none COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 15, 15, 12, 15, 15, 9, 9, 9, 9, 9, 9, 20, 20, 37, 38, 38, 38, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 15, 15, 15, 15, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38, 38, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617476206 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 Building ZINC001617476206 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617476206 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 72) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001617476206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617476206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001617476206 none COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 13, 13, 11, 13, 13, 8, 8, 8, 8, 8, 8, 19, 19, 39, 40, 40, 40, 8, 8, 8, 2, 8, 1, 1, 1, 2, 2, 1, 2, 2, 2, 15, 15, 15, 13, 13, 13, 13, 8, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 73) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001617476206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617476206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001617476206 none COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 15, 15, 12, 15, 15, 9, 9, 9, 9, 9, 9, 20, 20, 37, 38, 38, 38, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 15, 15, 15, 15, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38, 38, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617476206 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617476206 Building ZINC001617486110 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617486110 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/74 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2scc(c3cnn(C)c3)c2C(=O)OC(C)(C)C)c1) `ZINC001617486110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617486110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617486110 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2scc(c3cnn(C)c3)c2C(=O)OC(C)(C)C)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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 6, 6, 6, 21, 21, 21, 21, 21, 6, 6, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 2, 4, 4, 2, 6, 21, 21, 21, 21, 21, 19, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/75 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2scc(c3cnn(C)c3)c2C(=O)OC(C)(C)C)c1) `ZINC001617486110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617486110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617486110 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2scc(c3cnn(C)c3)c2C(=O)OC(C)(C)C)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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 6, 6, 6, 22, 22, 22, 22, 22, 6, 6, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 2, 4, 4, 2, 6, 22, 22, 22, 22, 22, 19, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617486110 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 Building ZINC001617486110 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617486110 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 74) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2scc(c3cnn(C)c3)c2C(=O)OC(C)(C)C)c1) `ZINC001617486110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617486110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617486110 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2scc(c3cnn(C)c3)c2C(=O)OC(C)(C)C)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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 6, 6, 6, 21, 21, 21, 21, 21, 6, 6, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 2, 4, 4, 2, 6, 21, 21, 21, 21, 21, 19, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 75) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2scc(c3cnn(C)c3)c2C(=O)OC(C)(C)C)c1) `ZINC001617486110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617486110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001617486110 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2scc(c3cnn(C)c3)c2C(=O)OC(C)(C)C)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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 6, 6, 6, 6, 22, 22, 22, 22, 22, 6, 6, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 2, 4, 4, 2, 6, 22, 22, 22, 22, 22, 19, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617486110 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486110 Building ZINC001617486416 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617486416 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/76 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1scc(c2cnn(C)c2)c1C(=O)OC(C)(C)C) `ZINC001617486416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617486416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001617486416 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1scc(c2cnn(C)c2)c1C(=O)OC(C)(C)C 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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 32, 32, 32, 32, 32, 9, 9, 31, 31, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 3, 9, 32, 32, 32, 32, 32, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/77 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1scc(c2cnn(C)c2)c1C(=O)OC(C)(C)C) `ZINC001617486416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617486416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001617486416 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1scc(c2cnn(C)c2)c1C(=O)OC(C)(C)C 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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 34, 34, 34, 34, 34, 9, 9, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 2, 2, 3, 9, 34, 34, 34, 34, 34, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617486416 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 Building ZINC001617486416 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617486416 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 76) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1scc(c2cnn(C)c2)c1C(=O)OC(C)(C)C) `ZINC001617486416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617486416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001617486416 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1scc(c2cnn(C)c2)c1C(=O)OC(C)(C)C 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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 32, 32, 32, 32, 32, 9, 9, 31, 31, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 3, 9, 32, 32, 32, 32, 32, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 77) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(F)cc1[C@]([O-])([SiH3])C(=O)Nc1scc(c2cnn(C)c2)c1C(=O)OC(C)(C)C) `ZINC001617486416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617486416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001617486416 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1scc(c2cnn(C)c2)c1C(=O)OC(C)(C)C 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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 34, 34, 34, 34, 34, 9, 9, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 2, 2, 3, 9, 34, 34, 34, 34, 34, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617486416 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617486416 Building ZINC001617542114 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617542114 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/78 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2c(cc1Br)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CC2) `ZINC001617542114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617542114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001617542114 none Cc1cc2c(cc1Br)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 2, 17, 1, 1, 1, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7, 7, 25, 25, 25, 25] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/79 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2c(cc1Br)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CC2) `ZINC001617542114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617542114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001617542114 none Cc1cc2c(cc1Br)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 2, 18, 1, 1, 1, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 26, 26, 26, 26] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617542114 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 Building ZINC001617542114 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617542114 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 78) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc2c(cc1Br)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CC2) `ZINC001617542114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617542114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001617542114 none Cc1cc2c(cc1Br)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 2, 17, 1, 1, 1, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7, 7, 25, 25, 25, 25] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 79) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc2c(cc1Br)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CC2) `ZINC001617542114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617542114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001617542114 none Cc1cc2c(cc1Br)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 2, 18, 1, 1, 1, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 26, 26, 26, 26] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617542114 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617542114 Building ZINC001617656764 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617656764 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/80 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCSCCOc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001617656764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617656764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001617656764 none O=C(NCCSCCOc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 6, 7, 11, 23, 31, 31, 31, 31, 31, 31, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 3, 3, 7, 7, 11, 11, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 16, 17, 18, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/81 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCSCCOc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001617656764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617656764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001617656764 none O=C(NCCSCCOc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 6, 7, 11, 22, 31, 31, 31, 31, 31, 31, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 3, 3, 7, 7, 11, 11, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 16, 17, 18, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617656764 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 Building ZINC001617656764 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617656764 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 80) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NCCSCCOc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001617656764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617656764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001617656764 none O=C(NCCSCCOc1cccc(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 6, 7, 11, 23, 31, 31, 31, 31, 31, 31, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 3, 3, 7, 7, 11, 11, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 16, 17, 18, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 81) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NCCSCCOc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001617656764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617656764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001617656764 none O=C(NCCSCCOc1cccc(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 5, 5, 12, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 6, 7, 11, 22, 31, 31, 31, 31, 31, 31, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 3, 3, 7, 7, 11, 11, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 16, 17, 18, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617656764 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617656764 Building ZINC001617760319 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617760319 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/82 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl) `ZINC001617760319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617760319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001617760319 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 14, 14, 21, 21, 26, 26, 26, 26, 3, 3, 3, 5, 5, 5, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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, 59, 60]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/83 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl) `ZINC001617760319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617760319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001617760319 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 10, 14, 14, 22, 22, 28, 28, 28, 28, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617760319 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 Building ZINC001617760319 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617760319 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 82) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl) `ZINC001617760319.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617760319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001617760319 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 14, 14, 21, 21, 26, 26, 26, 26, 3, 3, 3, 5, 5, 5, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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, 59, 60]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 83) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl) `ZINC001617760319.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617760319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001617760319 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 10, 14, 14, 22, 22, 28, 28, 28, 28, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617760319 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760319 Building ZINC001617760320 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617760320 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/84 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl) `ZINC001617760320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617760320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001617760320 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 24, 24, 28, 28, 28, 28, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/85 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl) `ZINC001617760320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617760320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001617760320 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 10, 10, 18, 18, 27, 27, 28, 28, 28, 28, 2, 2, 2, 4, 4, 4, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617760320 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 Building ZINC001617760320 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617760320 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 84) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl) `ZINC001617760320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617760320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001617760320 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 24, 24, 28, 28, 28, 28, 2, 2, 2, 6, 6, 6, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 85) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl) `ZINC001617760320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617760320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001617760320 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CCN(C)C(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 10, 10, 18, 18, 27, 27, 28, 28, 28, 28, 2, 2, 2, 4, 4, 4, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617760320 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617760320 Building ZINC001617870024 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617870024 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/86 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3)(N3CCCC3)CC2)cc1Cl) `ZINC001617870024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617870024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617870024 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3)(N3CCCC3)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', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 17, 17, 17, 16, 8, 8, 6, 6, 6, 12, 12, 12, 6, 6, 8, 8, 8, 8, 13, 13, 8, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/87 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3)(N3CCCC3)CC2)cc1Cl) `ZINC001617870024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617870024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617870024 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3)(N3CCCC3)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', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 17, 17, 17, 16, 8, 8, 6, 6, 6, 12, 12, 12, 6, 6, 8, 8, 8, 8, 13, 13, 8, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617870024 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 Building ZINC001617870024 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617870024 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 86) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3)(N3CCCC3)CC2)cc1Cl) `ZINC001617870024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617870024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617870024 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3)(N3CCCC3)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', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 17, 17, 17, 16, 8, 8, 6, 6, 6, 12, 12, 12, 6, 6, 8, 8, 8, 8, 13, 13, 8, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 87) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3)(N3CCCC3)CC2)cc1Cl) `ZINC001617870024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617870024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001617870024 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3ccccc3)(N3CCCC3)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', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 17, 17, 17, 16, 8, 8, 6, 6, 6, 12, 12, 12, 6, 6, 8, 8, 8, 8, 13, 13, 8, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617870024 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617870024 Building ZINC001617932701 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617932701 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/88 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1) `ZINC001617932701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617932701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001617932701 none O=C(N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 17, 17, 17, 17, 17, 17, 6, 2, 7, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 17, 36, 47, 47, 36, 37, 47, 47, 36, 17, 17, 17, 17, 17, 17, 4, 1, 4, 17, 17, 47, 47, 47, 47] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/89 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1) `ZINC001617932701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617932701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001617932701 none O=C(N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 19, 19, 19, 19, 19, 19, 7, 2, 9, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 37, 47, 47, 37, 37, 47, 47, 37, 19, 19, 19, 19, 19, 19, 4, 1, 4, 19, 19, 47, 47, 47, 47] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617932701 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 Building ZINC001617932701 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617932701 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 88) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1) `ZINC001617932701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617932701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001617932701 none O=C(N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 17, 17, 17, 17, 17, 17, 6, 2, 7, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 17, 36, 47, 47, 36, 37, 47, 47, 36, 17, 17, 17, 17, 17, 17, 4, 1, 4, 17, 17, 47, 47, 47, 47] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 89) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1) `ZINC001617932701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617932701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001617932701 none O=C(N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 19, 19, 19, 19, 19, 19, 7, 2, 9, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 19, 37, 47, 47, 37, 37, 47, 47, 37, 19, 19, 19, 19, 19, 19, 4, 1, 4, 19, 19, 47, 47, 47, 47] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617932701 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932701 Building ZINC001617932732 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617932732 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/90 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1) `ZINC001617932732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617932732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001617932732 none O=C(N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 18, 18, 18, 18, 18, 18, 10, 1, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 35, 46, 46, 36, 46, 46, 46, 35, 18, 18, 18, 18, 18, 18, 3, 1, 3, 18, 18, 46, 46, 46, 46] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/91 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1) `ZINC001617932732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617932732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001617932732 none O=C(N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 22, 22, 22, 22, 22, 22, 10, 1, 13, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 22, 37, 46, 46, 37, 46, 46, 46, 37, 22, 22, 22, 22, 22, 22, 4, 1, 4, 22, 22, 46, 46, 46, 46] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617932732 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 Building ZINC001617932732 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001617932732 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 90) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1) `ZINC001617932732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001617932732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001617932732 none O=C(N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 18, 18, 18, 18, 18, 18, 10, 1, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 35, 46, 46, 36, 46, 46, 46, 35, 18, 18, 18, 18, 18, 18, 3, 1, 3, 18, 18, 46, 46, 46, 46] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 91) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1) `ZINC001617932732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001617932732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001617932732 none O=C(N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 22, 22, 22, 22, 22, 22, 10, 1, 13, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 22, 37, 46, 46, 37, 46, 46, 46, 37, 22, 22, 22, 22, 22, 22, 4, 1, 4, 22, 22, 46, 46, 46, 46] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001617932732 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001617932732 Building ZINC001618000917 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618000917 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/92 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc(c2ccccc2F)cs1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618000917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618000917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001618000917 none O=C(NCc1nc(c2ccccc2F)cs1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 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, 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, 10, 32, 32, 32, 50, 50, 32, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 10, 50, 50, 50, 50, 32, 2, 2] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/93 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc(c2ccccc2F)cs1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618000917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618000917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001618000917 none O=C(NCc1nc(c2ccccc2F)cs1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 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, 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, 10, 32, 32, 32, 50, 50, 32, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 10, 50, 50, 50, 50, 32, 2, 2] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618000917 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 Building ZINC001618000917 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618000917 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 92) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc(c2ccccc2F)cs1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618000917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618000917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001618000917 none O=C(NCc1nc(c2ccccc2F)cs1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 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, 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, 10, 32, 32, 32, 50, 50, 32, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 10, 50, 50, 50, 50, 32, 2, 2] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 93) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc(c2ccccc2F)cs1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618000917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618000917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001618000917 none O=C(NCc1nc(c2ccccc2F)cs1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 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, 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, 10, 32, 32, 32, 50, 50, 32, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 10, 50, 50, 50, 50, 32, 2, 2] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618000917 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618000917 Building ZINC001618034722 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618034722 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/94 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1COc1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001618034722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618034722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001618034722 none O=C(N1CCC[C@H]1COc1ccc(Br)cc1)[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', 'H', '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', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 12, 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, 7, 7] dock color type numbers: [6, 9, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 13, 26, 27, 27, 26, 26, 27, 27, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 13, 13, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 70 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/95 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1COc1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001618034722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618034722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001618034722 none O=C(N1CCC[C@H]1COc1ccc(Br)cc1)[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', 'H', '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', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 12, 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, 7, 7] dock color type numbers: [6, 9, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 64 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618034722 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 Building ZINC001618034722 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618034722 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 94) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CCC[C@H]1COc1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001618034722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618034722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001618034722 none O=C(N1CCC[C@H]1COc1ccc(Br)cc1)[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', 'H', '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', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 12, 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, 7, 7] dock color type numbers: [6, 9, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 13, 26, 27, 27, 26, 26, 27, 27, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 13, 13, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 70 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 95) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CCC[C@H]1COc1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001618034722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618034722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001618034722 none O=C(N1CCC[C@H]1COc1ccc(Br)cc1)[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', 'H', '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', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 12, 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, 7, 7] dock color type numbers: [6, 9, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 64 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618034722 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618034722 Building ZINC001618061279 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618061279 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/96 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/96' -> `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@]1(C)CC1(F)F) `ZINC001618061279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618061279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001618061279 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@]1(C)CC1(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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 13, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 13, 13, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/97 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/97' -> `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@]1(C)CC1(F)F) `ZINC001618061279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618061279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001618061279 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@]1(C)CC1(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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 11, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 11, 11, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618061279 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 Building ZINC001618061279 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618061279 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 96) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@]1(C)CC1(F)F) `ZINC001618061279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618061279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001618061279 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@]1(C)CC1(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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 13, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 13, 13, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 97) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@]1(C)CC1(F)F) `ZINC001618061279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618061279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001618061279 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@]1(C)CC1(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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 11, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 11, 11, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618061279 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061279 Building ZINC001618061292 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618061292 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/98 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/98' -> `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@@]1(C)CC1(F)F) `ZINC001618061292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618061292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001618061292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@]1(C)CC1(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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 11, 13, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 13, 13, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/99 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/99' -> `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@@]1(C)CC1(F)F) `ZINC001618061292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618061292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001618061292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@]1(C)CC1(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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 13, 14, 14, 14, 14, 14, 3, 3, 3, 11, 11, 6, 11, 3, 3, 3, 2, 10, 10, 13, 13, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618061292 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 Building ZINC001618061292 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618061292 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 98) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@]1(C)CC1(F)F) `ZINC001618061292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618061292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001618061292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@]1(C)CC1(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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 11, 13, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 13, 13, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 99) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@]1(C)CC1(F)F) `ZINC001618061292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618061292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001618061292 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@]1(C)CC1(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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 13, 14, 14, 14, 14, 14, 3, 3, 3, 11, 11, 6, 11, 3, 3, 3, 2, 10, 10, 13, 13, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618061292 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618061292 Building ZINC001618104980 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618104980 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/100 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1) `ZINC001618104980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618104980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618104980 none Cc1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 13, 31, 31, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 12, 12, 14, 14, 14, 14, 31, 31, 31, 31, 18, 31, 31, 4, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/101 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1) `ZINC001618104980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618104980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618104980 none Cc1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 13, 13, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 4, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618104980 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 Building ZINC001618104980 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618104980 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 100) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1) `ZINC001618104980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618104980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618104980 none Cc1cccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 13, 31, 31, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 12, 12, 14, 14, 14, 14, 31, 31, 31, 31, 18, 31, 31, 4, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 101) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1) `ZINC001618104980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618104980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618104980 none Cc1cccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 13, 13, 16, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 4, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618104980 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104980 Building ZINC001618104981 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618104981 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/102 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1) `ZINC001618104981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618104981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618104981 none Cc1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 13, 23, 23, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 12, 12, 15, 15, 15, 15, 23, 23, 23, 23, 16, 23, 23, 4, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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: 102 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/103 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1) `ZINC001618104981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618104981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618104981 none Cc1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 13, 30, 30, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 11, 11, 13, 13, 13, 13, 30, 30, 30, 30, 18, 30, 30, 4, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 30] 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: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618104981 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 Building ZINC001618104981 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618104981 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 102) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1) `ZINC001618104981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618104981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618104981 none Cc1cccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 13, 23, 23, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 12, 12, 15, 15, 15, 15, 23, 23, 23, 23, 16, 23, 23, 4, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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: 102 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 103) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1) `ZINC001618104981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618104981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618104981 none Cc1cccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 13, 30, 30, 7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 11, 11, 13, 13, 13, 13, 30, 30, 30, 30, 18, 30, 30, 4, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 30] 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: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618104981 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618104981 Building ZINC001618105113 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618105113 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/104 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2ccc(I)cc2)c1) `ZINC001618105113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618105113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001618105113 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2ccc(I)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 1, 1, 1, 18, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/105 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2ccc(I)cc2)c1) `ZINC001618105113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618105113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001618105113 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2ccc(I)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 1, 1, 1, 18, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 8, 8, 1, 1, 1, 1, 6, 8, 14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 1, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 8] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618105113 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 Building ZINC001618105113 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618105113 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 104) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2ccc(I)cc2)c1) `ZINC001618105113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618105113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001618105113 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2ccc(I)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 1, 1, 1, 18, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 105) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2ccc(I)cc2)c1) `ZINC001618105113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618105113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001618105113 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@]2(C)Cc2ccc(I)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 1, 1, 1, 18, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 8, 8, 1, 1, 1, 1, 6, 8, 14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 1, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 8] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618105113 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105113 Building ZINC001618105114 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618105114 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/106 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2ccc(I)cc2)c1) `ZINC001618105114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618105114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001618105114 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2ccc(I)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 1, 1, 1, 18, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 6, 8, 14, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/107 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2ccc(I)cc2)c1) `ZINC001618105114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618105114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001618105114 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2ccc(I)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 1, 1, 1, 18, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 1, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/369383/xbb-8058088.28/working/building/ZINC001618105114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618105114 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114 Building ZINC001618105114 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618105114 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 106) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2ccc(I)cc2)c1) `ZINC001618105114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618105114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001618105114 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2ccc(I)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 1, 1, 1, 18, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 6, 8, 14, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 107) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2ccc(I)cc2)c1) `ZINC001618105114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618105114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001618105114 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCC[C@]2(C)Cc2ccc(I)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 1, 1, 1, 18, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 1, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/369383/xbb-8058088.28/working/building/ZINC001618105114 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618105114 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618105114 Building ZINC001618138489 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618138489 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/108 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(F)ccc(Br)c1F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618138489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618138489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618138489 none O=C(Nc1c(F)ccc(Br)c1F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 1, 17, 1, 15, 5, 12, 1, 1, 1, 1, 17, 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: [6, 1, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 6, 24, 24, 10, 10] 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: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/109 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(F)ccc(Br)c1F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618138489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618138489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618138489 none O=C(Nc1c(F)ccc(Br)c1F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 1, 17, 1, 15, 5, 12, 1, 1, 1, 1, 17, 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: [6, 1, 6, 6, 24, 24, 24, 20, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 6, 24, 20, 10, 10] 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: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618138489 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 Building ZINC001618138489 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618138489 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 108) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(Nc1c(F)ccc(Br)c1F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618138489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618138489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618138489 none O=C(Nc1c(F)ccc(Br)c1F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 1, 17, 1, 15, 5, 12, 1, 1, 1, 1, 17, 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: [6, 1, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 6, 24, 24, 10, 10] 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: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 109) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(Nc1c(F)ccc(Br)c1F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618138489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618138489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618138489 none O=C(Nc1c(F)ccc(Br)c1F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 1, 17, 1, 15, 5, 12, 1, 1, 1, 1, 17, 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: [6, 1, 6, 6, 24, 24, 24, 20, 24, 24, 24, 24, 1, 1, 1, 10, 10, 10, 10, 10, 6, 24, 20, 10, 10] 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: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618138489 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618138489 Building ZINC001618147746 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618147746 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/110 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(OC(F)(F)F)ccc2Br)cn1) `ZINC001618147746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618147746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618147746 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(OC(F)(F)F)ccc2Br)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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'N.2', '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, 12, 5, 15, 15, 15, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 25, 26, 26, 26, 4, 4, 4, 4, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 4, 4, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/111 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(OC(F)(F)F)ccc2Br)cn1) `ZINC001618147746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618147746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618147746 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(OC(F)(F)F)ccc2Br)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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'N.2', '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, 12, 5, 15, 15, 15, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 25, 26, 26, 26, 4, 4, 4, 4, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 4, 4, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618147746 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 Building ZINC001618147746 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618147746 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 110) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(OC(F)(F)F)ccc2Br)cn1) `ZINC001618147746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618147746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618147746 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(OC(F)(F)F)ccc2Br)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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'N.2', '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, 12, 5, 15, 15, 15, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 25, 26, 26, 26, 4, 4, 4, 4, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 4, 4, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 111) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(OC(F)(F)F)ccc2Br)cn1) `ZINC001618147746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618147746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001618147746 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(OC(F)(F)F)ccc2Br)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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'N.2', '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, 12, 5, 15, 15, 15, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 25, 26, 26, 26, 4, 4, 4, 4, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 4, 4, 4, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618147746 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618147746 Building ZINC001618189559 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618189559 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/112 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](c2cccc(Cl)c2)OCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618189559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618189559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001618189559 none C[C@H]1[C@H](c2cccc(Cl)c2)OCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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, 5, 7, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 27, 28, 28, 28, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/113 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](c2cccc(Cl)c2)OCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618189559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618189559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001618189559 none C[C@H]1[C@H](c2cccc(Cl)c2)OCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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, 5, 7, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 12, 12, 12, 10, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 32, 32, 32, 32, 12, 12, 12, 12, 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]) total number of confs: 63 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618189559 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 Building ZINC001618189559 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618189559 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 112) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1[C@H](c2cccc(Cl)c2)OCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618189559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618189559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001618189559 none C[C@H]1[C@H](c2cccc(Cl)c2)OCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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, 5, 7, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 27, 28, 28, 28, 11, 11, 11, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 28, 28, 28, 28, 11, 11, 11, 11, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 113) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1[C@H](c2cccc(Cl)c2)OCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618189559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618189559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001618189559 none C[C@H]1[C@H](c2cccc(Cl)c2)OCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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, 5, 7, 5, 7, 1, 1, 1, 1, 1, 16, 1, 12, 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, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 12, 12, 12, 10, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 32, 32, 32, 32, 12, 12, 12, 12, 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]) total number of confs: 63 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618189559 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618189559 Building ZINC001618198127 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618198127 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/114 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC001618198127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618198127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001618198127 none CSCC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 13, 13, 13, 9, 9, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/115 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC001618198127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618198127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001618198127 none CSCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 10, 10, 10, 9, 9, 3, 3, 3, 3, 3, 2, 2, 2, 8, 8, 3, 8, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618198127 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 Building ZINC001618198127 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618198127 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 114) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CSCC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC001618198127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618198127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001618198127 none CSCC1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 13, 13, 13, 9, 9, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 115) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CSCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC001618198127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618198127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001618198127 none CSCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 10, 10, 10, 9, 9, 3, 3, 3, 3, 3, 2, 2, 2, 8, 8, 3, 8, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618198127 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618198127 Building ZINC001618348851 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618348851 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/116 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2cc1OC) `ZINC001618348851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618348851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001618348851 none COc1cc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 11, 11, 11, 11, 11, 27, 22, 22, 22, 11, 11, 11, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 11, 11, 27, 27, 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, 50, 51, 52, 53, 54]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/117 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2cc1OC) `ZINC001618348851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618348851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001618348851 none COc1cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 12, 12, 12, 12, 12, 28, 22, 22, 22, 12, 12, 12, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 12, 12, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618348851 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 Building ZINC001618348851 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618348851 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 116) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2cc1OC) `ZINC001618348851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618348851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001618348851 none COc1cc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 11, 11, 11, 11, 11, 27, 22, 22, 22, 11, 11, 11, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 11, 11, 27, 27, 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, 50, 51, 52, 53, 54]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 117) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2cc1OC) `ZINC001618348851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618348851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001618348851 none COc1cc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 12, 12, 12, 12, 12, 28, 22, 22, 22, 12, 12, 12, 2, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 12, 12, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618348851 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618348851 Building ZINC001618631234 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618631234 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/118 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CCNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc(OC)c1OCc1ccccc1) `ZINC001618631234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618631234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001618631234 none COc1cc(CCNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc(OC)c1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 6, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 9, 9, 9, 11, 6, 9, 10, 23, 29, 29, 25, 29, 29, 12, 12, 12, 9, 6, 6, 4, 4, 2, 4, 4, 2, 4, 4, 4, 4, 9, 11, 11, 11, 23, 23, 29, 29, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/119 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CCNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc(OC)c1OCc1ccccc1) `ZINC001618631234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618631234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001618631234 none COc1cc(CCNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc(OC)c1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 5, 3, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 8, 8, 8, 11, 8, 8, 9, 22, 28, 28, 26, 28, 28, 11, 11, 11, 8, 5, 5, 3, 3, 2, 4, 4, 2, 4, 4, 4, 4, 8, 11, 11, 11, 22, 22, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618631234 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 Building ZINC001618631234 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618631234 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 118) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CCNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc(OC)c1OCc1ccccc1) `ZINC001618631234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618631234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001618631234 none COc1cc(CCNC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc(OC)c1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 6, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 9, 9, 9, 11, 6, 9, 10, 23, 29, 29, 25, 29, 29, 12, 12, 12, 9, 6, 6, 4, 4, 2, 4, 4, 2, 4, 4, 4, 4, 9, 11, 11, 11, 23, 23, 29, 29, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 119) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CCNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc(OC)c1OCc1ccccc1) `ZINC001618631234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618631234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001618631234 none COc1cc(CCNC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc(OC)c1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 5, 3, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 8, 8, 8, 11, 8, 8, 9, 22, 28, 28, 26, 28, 28, 11, 11, 11, 8, 5, 5, 3, 3, 2, 4, 4, 2, 4, 4, 4, 4, 8, 11, 11, 11, 22, 22, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618631234 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618631234 Building ZINC001618709184 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618709184 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/120 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(OCc2cccc3ccccc32)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618709184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618709184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001618709184 none O=C(N1CC(OCc2cccc3ccccc32)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 4, 4, 4, 16, 24, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 24, 24, 43, 43, 43, 43, 43, 43, 43, 4, 4, 3, 3] 50 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([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: 93 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/121 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(OCc2cccc3ccccc32)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618709184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618709184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001618709184 none O=C(N1CC(OCc2cccc3ccccc32)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 5, 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, 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] 0 hydrogens need rotated 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, 16, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 25, 25, 44, 44, 44, 44, 44, 44, 44, 4, 4, 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: 100 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618709184 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 Building ZINC001618709184 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618709184 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 120) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(OCc2cccc3ccccc32)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618709184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618709184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001618709184 none O=C(N1CC(OCc2cccc3ccccc32)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 4, 4, 4, 16, 24, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 24, 24, 43, 43, 43, 43, 43, 43, 43, 4, 4, 3, 3] 50 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([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: 93 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 121) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(OCc2cccc3ccccc32)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001618709184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618709184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001618709184 none O=C(N1CC(OCc2cccc3ccccc32)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 5, 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, 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] 0 hydrogens need rotated 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, 16, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 25, 25, 44, 44, 44, 44, 44, 44, 44, 4, 4, 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: 100 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618709184 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618709184 Building ZINC001618807484 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618807484 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/122 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/122' -> `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)NCCC1SCCS1) `ZINC001618807484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618807484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001618807484 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC1SCCS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 14, 5, 5, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 11, 16, 16, 16, 16, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 9, 9, 11, 11, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/123 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/123' -> `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)NCCC1SCCS1) `ZINC001618807484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618807484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001618807484 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC1SCCS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 14, 5, 5, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 10, 10, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618807484 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 Building ZINC001618807484 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001618807484 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 122) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC1SCCS1) `ZINC001618807484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001618807484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001618807484 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCC1SCCS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 14, 5, 5, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 11, 16, 16, 16, 16, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 9, 9, 11, 11, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 123) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC1SCCS1) `ZINC001618807484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001618807484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001618807484 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCC1SCCS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 14, 5, 5, 14, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 10, 10, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001618807484 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001618807484 Building ZINC000016233466 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016233466 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/124 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/124' -> `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(OCC#N)cc1) `ZINC000016233466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016233466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016233466 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCC#N)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 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, 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, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 11, 14, 14, 4, 4, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 4, 4, 14, 14, 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]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/125 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/125' -> `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(OCC#N)cc1) `ZINC000016233466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016233466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016233466 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(OCC#N)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 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, 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, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 13, 14, 14, 4, 4, 3, 3, 3, 15, 15, 5, 15, 3, 3, 3, 2, 4, 4, 14, 14, 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]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC000016233466 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 Building ZINC000016233466 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016233466 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 124) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCC#N)cc1) `ZINC000016233466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016233466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016233466 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCC#N)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 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, 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, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 11, 14, 14, 4, 4, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 4, 4, 14, 14, 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]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 125) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(OCC#N)cc1) `ZINC000016233466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016233466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016233466 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(OCC#N)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.1', 'N.1', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 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, 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, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 13, 14, 14, 4, 4, 3, 3, 3, 15, 15, 5, 15, 3, 3, 3, 2, 4, 4, 14, 14, 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]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC000016233466 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC000016233466 Building ZINC001621255112 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001621255112 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/126 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2cccc(OC)c2)c1) `ZINC001621255112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001621255112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001621255112 none COc1cccc(C(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2cccc(OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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: [15, 15, 15, 15, 15, 15, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 17, 17, 17, 17, 17, 19, 17, 15, 15, 15, 15, 15, 15, 15, 6, 3, 4, 4, 4, 4, 17, 17, 17, 19, 19, 19, 17, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/127 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2cccc(OC)c2)c1) `ZINC001621255112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001621255112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001621255112 none COc1cccc(C(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2cccc(OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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: [20, 18, 18, 18, 18, 18, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 14, 14, 14, 14, 14, 14, 14, 18, 20, 20, 20, 18, 18, 18, 6, 3, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001621255112 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 Building ZINC001621255112 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001621255112 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 126) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1cccc(C(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2cccc(OC)c2)c1) `ZINC001621255112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001621255112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001621255112 none COc1cccc(C(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2cccc(OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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: [15, 15, 15, 15, 15, 15, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 17, 17, 17, 17, 17, 19, 17, 15, 15, 15, 15, 15, 15, 15, 6, 3, 4, 4, 4, 4, 17, 17, 17, 19, 19, 19, 17, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 127) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1cccc(C(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2cccc(OC)c2)c1) `ZINC001621255112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001621255112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001621255112 none COc1cccc(C(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2cccc(OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 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: [20, 18, 18, 18, 18, 18, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 14, 14, 14, 14, 14, 14, 14, 18, 20, 20, 20, 18, 18, 18, 6, 3, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001621255112 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001621255112 Building ZINC001622013423 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001622013423 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/128 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3cccc(OC(F)(F)F)c3)C2)cc1Cl) `ZINC001622013423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001622013423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001622013423 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3cccc(OC(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 8, 8, 8, 8, 8, 34, 34, 34, 34, 8, 2, 2, 2, 2, 5, 5, 5, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 8, 2, 2, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/129 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3cccc(OC(F)(F)F)c3)C2)cc1Cl) `ZINC001622013423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001622013423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001622013423 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3cccc(OC(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 2, 5, 7, 7, 7, 7, 7, 28, 28, 28, 28, 7, 2, 2, 2, 2, 4, 4, 4, 2, 2, 2, 2, 2, 5, 5, 7, 7, 7, 7, 2, 2, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001622013423 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 Building ZINC001622013423 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001622013423 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 128) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3cccc(OC(F)(F)F)c3)C2)cc1Cl) `ZINC001622013423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001622013423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001622013423 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3cccc(OC(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 8, 8, 8, 8, 8, 34, 34, 34, 34, 8, 2, 2, 2, 2, 5, 5, 5, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 8, 2, 2, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 129) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3cccc(OC(F)(F)F)c3)C2)cc1Cl) `ZINC001622013423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001622013423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001622013423 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3cccc(OC(F)(F)F)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 2, 5, 7, 7, 7, 7, 7, 28, 28, 28, 28, 7, 2, 2, 2, 2, 4, 4, 4, 2, 2, 2, 2, 2, 5, 5, 7, 7, 7, 7, 2, 2, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001622013423 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001622013423 Building ZINC001623323695 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623323695 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/130 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2nc3ccncc3[nH]2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623323695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623323695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001623323695 none O=C(Nc1ccc(c2nc3ccncc3[nH]2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 6, 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, 3, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 4, 6, 39, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 4, 9, 9, 39, 39, 39, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/131 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2nc3ccncc3[nH]2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623323695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623323695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001623323695 none O=C(Nc1ccc(c2nc3ccncc3[nH]2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 6, 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, 3, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 4, 6, 36, 40, 40, 40, 40, 40, 40, 40, 39, 8, 8, 1, 1, 1, 10, 10, 10, 10, 10, 4, 8, 8, 40, 40, 40, 8, 8, 10, 10] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623323695 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 Building ZINC001623323695 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623323695 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 130) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(Nc1ccc(c2nc3ccncc3[nH]2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623323695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623323695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001623323695 none O=C(Nc1ccc(c2nc3ccncc3[nH]2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 6, 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, 3, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 4, 6, 39, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 4, 9, 9, 39, 39, 39, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 131) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(Nc1ccc(c2nc3ccncc3[nH]2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623323695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623323695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001623323695 none O=C(Nc1ccc(c2nc3ccncc3[nH]2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 6, 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, 3, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 4, 6, 36, 40, 40, 40, 40, 40, 40, 40, 39, 8, 8, 1, 1, 1, 10, 10, 10, 10, 10, 4, 8, 8, 40, 40, 40, 8, 8, 10, 10] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623323695 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623323695 Building ZINC001623353951 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623353951 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/132 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@H]1CCc2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001623353951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623353951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623353951 none CN(C)[C@H]1CCc2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 19, 24, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 14, 3, 14, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 19, 24, 24, 24, 24, 24, 24, 19, 19, 19, 19, 19, 19, 19, 6, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 100 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/133 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@H]1CCc2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001623353951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623353951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623353951 none CN(C)[C@H]1CCc2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 27, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 2, 13, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 19, 27, 27, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 19, 6, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623353951 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 Building ZINC001623353951 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623353951 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 132) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C)[C@H]1CCc2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001623353951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623353951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623353951 none CN(C)[C@H]1CCc2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 19, 24, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 14, 3, 14, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 19, 24, 24, 24, 24, 24, 24, 19, 19, 19, 19, 19, 19, 19, 6, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 100 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 133) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C)[C@H]1CCc2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001623353951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623353951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623353951 none CN(C)[C@H]1CCc2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 27, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 2, 13, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 19, 27, 27, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 19, 6, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623353951 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353951 Building ZINC001623353952 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623353952 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/134 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H]1CCc2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001623353952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623353952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623353952 none CN(C)[C@@H]1CCc2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 27, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 14, 3, 14, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 21, 27, 27, 27, 27, 27, 27, 21, 21, 21, 21, 21, 21, 21, 6, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 103 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/135 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)[C@@H]1CCc2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001623353952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623353952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623353952 none CN(C)[C@@H]1CCc2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 3, 16, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 21, 26, 26, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21, 21, 6, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623353952 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 Building ZINC001623353952 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623353952 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 134) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C)[C@@H]1CCc2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001623353952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623353952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623353952 none CN(C)[C@@H]1CCc2cc(Br)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 27, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 14, 3, 14, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 21, 27, 27, 27, 27, 27, 27, 21, 21, 21, 21, 21, 21, 21, 6, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 103 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 135) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C)[C@@H]1CCc2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC001623353952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623353952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623353952 none CN(C)[C@@H]1CCc2cc(Br)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', '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', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 16, 3, 16, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 21, 26, 26, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21, 21, 6, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623353952 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623353952 Building ZINC001623355624 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623355624 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/136 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(CCc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001623355624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623355624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623355624 none COc1ccc(CN(CCc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', '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', '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, 12, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 9, 19, 19, 9, 5, 3, 5, 10, 10, 20, 20, 20, 20, 20, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 9, 9, 10, 10, 10, 10, 20, 20, 20, 20, 5, 5, 5, 5, 19, 19] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/137 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(CCc2ccccn2)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001623355624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623355624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623355624 none COc1ccc(CN(CCc2ccccn2)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', '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', '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, 12, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 19, 19, 10, 5, 3, 5, 10, 10, 21, 21, 21, 21, 21, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 5, 5, 5, 5, 19, 19] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623355624 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 Building ZINC001623355624 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623355624 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 136) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(CN(CCc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001623355624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623355624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623355624 none COc1ccc(CN(CCc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', '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', '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, 12, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 9, 19, 19, 9, 5, 3, 5, 10, 10, 20, 20, 20, 20, 20, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 9, 9, 10, 10, 10, 10, 20, 20, 20, 20, 5, 5, 5, 5, 19, 19] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 137) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(CN(CCc2ccccn2)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001623355624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623355624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623355624 none COc1ccc(CN(CCc2ccccn2)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', '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', '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, 12, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 19, 19, 10, 5, 3, 5, 10, 10, 21, 21, 21, 21, 21, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 5, 5, 5, 5, 19, 19] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623355624 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623355624 Building ZINC001623395926 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623395926 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/138 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2nc(C(F)(F)F)cs2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623395926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623395926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623395926 none O=C(N1CCC[C@H](c2nc(C(F)(F)F)cs2)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', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 5, 15, 15, 15, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/139 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](c2nc(C(F)(F)F)cs2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623395926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623395926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623395926 none O=C(N1CCC[C@H](c2nc(C(F)(F)F)cs2)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', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 5, 15, 15, 15, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 33, 9, 9, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623395926 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 Building ZINC001623395926 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623395926 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 138) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@H](c2nc(C(F)(F)F)cs2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623395926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623395926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623395926 none O=C(N1CCC[C@H](c2nc(C(F)(F)F)cs2)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', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 5, 15, 15, 15, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 139) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@H](c2nc(C(F)(F)F)cs2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623395926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623395926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623395926 none O=C(N1CCC[C@H](c2nc(C(F)(F)F)cs2)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', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 5, 15, 15, 15, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 33, 9, 9, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623395926 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395926 Building ZINC001623395929 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623395929 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/140 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2nc(C(F)(F)F)cs2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623395929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623395929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623395929 none O=C(N1CCC[C@@H](c2nc(C(F)(F)F)cs2)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', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 5, 15, 15, 15, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 31, 9, 9, 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, 43]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/141 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](c2nc(C(F)(F)F)cs2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623395929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623395929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623395929 none O=C(N1CCC[C@@H](c2nc(C(F)(F)F)cs2)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', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 5, 15, 15, 15, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 23, 5, 5, 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, 43]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623395929 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 Building ZINC001623395929 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623395929 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 140) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@@H](c2nc(C(F)(F)F)cs2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623395929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623395929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623395929 none O=C(N1CCC[C@@H](c2nc(C(F)(F)F)cs2)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', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 5, 15, 15, 15, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 31, 9, 9, 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, 43]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 141) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@@H](c2nc(C(F)(F)F)cs2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623395929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623395929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623395929 none O=C(N1CCC[C@@H](c2nc(C(F)(F)F)cs2)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', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 5, 15, 15, 15, 1, 14, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 23, 5, 5, 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, 43]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623395929 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623395929 Building ZINC001623431419 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623431419 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/142 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/142' -> `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)Nc1nn(C)c2ccccc12) `ZINC001623431419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623431419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001623431419 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nn(C)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.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', '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', 'H', 'H'] dock atom 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, 8, 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] dock 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 5, 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/143 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/143' -> `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)Nc1nn(C)c2ccccc12) `ZINC001623431419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623431419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001623431419 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nn(C)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.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', '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', 'H', 'H'] dock atom 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, 8, 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] dock 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 21, 21, 7, 21, 4, 4, 4, 5, 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]) total number of confs: 74 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623431419 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 Building ZINC001623431419 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623431419 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 142) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nn(C)c2ccccc12) `ZINC001623431419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623431419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001623431419 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nn(C)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.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', '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', 'H', 'H'] dock atom 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, 8, 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] dock 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 5, 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]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 143) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nn(C)c2ccccc12) `ZINC001623431419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623431419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001623431419 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nn(C)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.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', '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', 'H', 'H'] dock atom 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, 8, 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] dock 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 21, 21, 7, 21, 4, 4, 4, 5, 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]) total number of confs: 74 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623431419 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623431419 Building ZINC001623454008 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623454008 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/144 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3Br)no2)CC1) `ZINC001623454008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623454008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001623454008 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3Br)no2)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.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 4, 4, 4, 4, 4, 12, 12, 12, 18, 18, 12, 18, 18, 18, 12, 12, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 18, 18, 16, 18, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/145 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3Br)no2)CC1) `ZINC001623454008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623454008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001623454008 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3Br)no2)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.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 4, 5, 5, 5, 5, 11, 11, 11, 17, 17, 11, 17, 17, 17, 11, 11, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 17, 17, 13, 17, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623454008 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 Building ZINC001623454008 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623454008 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 144) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3Br)no2)CC1) `ZINC001623454008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623454008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001623454008 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3Br)no2)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.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 4, 4, 4, 4, 4, 12, 12, 12, 18, 18, 12, 18, 18, 18, 12, 12, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 18, 18, 16, 18, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 145) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3Br)no2)CC1) `ZINC001623454008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623454008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001623454008 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3Br)no2)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.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 4, 5, 5, 5, 5, 11, 11, 11, 17, 17, 11, 17, 17, 17, 11, 11, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 17, 17, 13, 17, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623454008 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623454008 Building ZINC001623557212 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623557212 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/146 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C(=O)OC(C)(C)C)cn1) `ZINC001623557212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623557212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001623557212 none Cn1cc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)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', 'F', '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, 15, 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, 2, 2, 2, 2, 7, 7, 32, 32, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 7, 3, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 33, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/147 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C(=O)OC(C)(C)C)cn1) `ZINC001623557212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623557212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001623557212 none Cn1cc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)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', 'F', '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, 15, 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: [25, 25, 25, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 31, 31, 32, 32, 32, 32, 25, 25, 25, 25, 25, 25, 7, 3, 2, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623557212 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 Building ZINC001623557212 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623557212 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 146) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cn1cc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C(=O)OC(C)(C)C)cn1) `ZINC001623557212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623557212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001623557212 none Cn1cc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)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', 'F', '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, 15, 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, 2, 2, 2, 2, 7, 7, 32, 32, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 7, 3, 2, 2, 2, 2, 33, 33, 33, 33, 33, 33, 33, 33, 33, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 147) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cn1cc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C(=O)OC(C)(C)C)cn1) `ZINC001623557212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623557212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001623557212 none Cn1cc(c2csc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)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', 'F', '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, 15, 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: [25, 25, 25, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 31, 31, 32, 32, 32, 32, 25, 25, 25, 25, 25, 25, 7, 3, 2, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 25] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623557212 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623557212 Building ZINC001623594514 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623594514 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/148 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/148' -> `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]1CCOCC12CCCC2) `ZINC001623594514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623594514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623594514 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2, 3, 14, 14, 14, 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, 56, 57]) total number of confs: 80 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/149 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/149' -> `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]1CCOCC12CCCC2) `ZINC001623594514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623594514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623594514 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 15, 15, 7, 15, 15, 15, 15, 15, 15, 2, 2, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 15, 15, 13, 15, 2, 2, 2, 4, 12, 12, 12, 12, 12, 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, 57]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623594514 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 Building ZINC001623594514 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623594514 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 148) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOCC12CCCC2) `ZINC001623594514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623594514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623594514 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2, 3, 14, 14, 14, 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, 56, 57]) total number of confs: 80 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 149) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOCC12CCCC2) `ZINC001623594514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623594514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623594514 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 15, 15, 7, 15, 15, 15, 15, 15, 15, 2, 2, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 15, 15, 13, 15, 2, 2, 2, 4, 12, 12, 12, 12, 12, 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, 57]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623594514 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594514 Building ZINC001623594515 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623594515 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/150 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/150' -> `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]1CCOCC12CCCC2) `ZINC001623594515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623594515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623594515 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 14, 14, 6, 14, 2, 2, 2, 4, 12, 12, 12, 12, 12, 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, 57]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/151 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/151' -> `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]1CCOCC12CCCC2) `ZINC001623594515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623594515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623594515 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 3, 14, 14, 14, 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, 56, 57]) total number of confs: 84 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623594515 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 Building ZINC001623594515 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623594515 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 150) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOCC12CCCC2) `ZINC001623594515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623594515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623594515 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 14, 14, 6, 14, 2, 2, 2, 4, 12, 12, 12, 12, 12, 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, 57]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 151) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOCC12CCCC2) `ZINC001623594515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623594515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623594515 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 3, 14, 14, 14, 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, 56, 57]) total number of confs: 84 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623594515 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623594515 Building ZINC001623603245 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623603245 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/152 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623603245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623603245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623603245 none O=C(NC[C@@H](c1ccccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 10, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 31, 31, 31, 31, 1, 1, 1, 9, 9, 9, 9, 9, 4, 17, 17, 30, 30, 30, 30, 31, 31, 31, 31, 31, 31, 31, 31, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/153 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623603245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623603245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623603245 none O=C(NC[C@@H](c1ccccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 10, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 34, 35, 35, 34, 35, 35, 35, 34, 35, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 4, 16, 16, 35, 35, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623603245 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 Building ZINC001623603245 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623603245 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 152) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@@H](c1ccccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623603245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623603245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623603245 none O=C(NC[C@@H](c1ccccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 10, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 31, 31, 31, 31, 1, 1, 1, 9, 9, 9, 9, 9, 4, 17, 17, 30, 30, 30, 30, 31, 31, 31, 31, 31, 31, 31, 31, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 153) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@@H](c1ccccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623603245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623603245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623603245 none O=C(NC[C@@H](c1ccccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 10, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 34, 35, 35, 34, 35, 35, 35, 34, 35, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 4, 16, 16, 35, 35, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623603245 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603245 Building ZINC001623603246 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623603246 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/154 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623603246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623603246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623603246 none O=C(NC[C@H](c1ccccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 10, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 34, 36, 36, 34, 36, 36, 36, 34, 35, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 4, 16, 16, 36, 36, 35, 36, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/155 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623603246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623603246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623603246 none O=C(NC[C@H](c1ccccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 10, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 31, 31, 31, 31, 31, 31, 31, 31, 31, 32, 32, 32, 32, 1, 1, 1, 8, 8, 8, 8, 8, 4, 16, 16, 31, 31, 31, 31, 32, 32, 32, 32, 32, 32, 32, 32, 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, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623603246 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 Building ZINC001623603246 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623603246 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 154) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@H](c1ccccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623603246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623603246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623603246 none O=C(NC[C@H](c1ccccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 10, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 34, 36, 36, 34, 36, 36, 36, 34, 35, 35, 35, 35, 1, 1, 1, 8, 8, 8, 8, 8, 4, 16, 16, 36, 36, 35, 36, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 155) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@H](c1ccccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623603246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623603246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001623603246 none O=C(NC[C@H](c1ccccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 16, 10, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 31, 31, 31, 31, 31, 31, 31, 31, 31, 32, 32, 32, 32, 1, 1, 1, 8, 8, 8, 8, 8, 4, 16, 16, 31, 31, 31, 31, 32, 32, 32, 32, 32, 32, 32, 32, 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, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623603246 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623603246 Building ZINC001623613841 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623613841 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/156 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2cccnc2Oc2cccc(C(F)(F)F)c2)cn1) `ZINC001623613841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623613841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001623613841 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2cccnc2Oc2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 22, 22, 22, 22, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 22, 22, 22, 44, 44, 44, 44, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/157 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2cccnc2Oc2cccc(C(F)(F)F)c2)cn1) `ZINC001623613841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623613841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001623613841 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2cccnc2Oc2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 5, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 22, 22, 22, 22, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 11, 11, 22, 22, 22, 44, 44, 44, 44, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623613841 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 Building ZINC001623613841 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623613841 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 156) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2cccnc2Oc2cccc(C(F)(F)F)c2)cn1) `ZINC001623613841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623613841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001623613841 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2cccnc2Oc2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 22, 22, 22, 22, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 22, 22, 22, 44, 44, 44, 44, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 157) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2cccnc2Oc2cccc(C(F)(F)F)c2)cn1) `ZINC001623613841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623613841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001623613841 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2cccnc2Oc2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 5, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 22, 22, 22, 22, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 11, 11, 22, 22, 22, 44, 44, 44, 44, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623613841 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623613841 Building ZINC001623633463 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623633463 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/158 `/scratch/xiaobo/369383/xbb-8058088.28/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]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001623633463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623633463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623633463 none CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 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, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 49, 19, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 19, 19, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [54, 55, 56, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 57, 58, 59, 60]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/159 `/scratch/xiaobo/369383/xbb-8058088.28/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]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001623633463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623633463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623633463 none CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 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, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 39, 48, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [54, 55, 56, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 57, 58, 59, 60]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623633463 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 Building ZINC001623633463 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623633463 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 158) grep: /scratch/xiaobo/369383/xbb-8058088.28/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]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001623633463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623633463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623633463 none CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 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, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 49, 19, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 19, 19, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [54, 55, 56, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 57, 58, 59, 60]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 159) grep: /scratch/xiaobo/369383/xbb-8058088.28/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]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001623633463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623633463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623633463 none CC(C)(C)OC(=O)NC[C@@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 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, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 39, 48, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 20, 20, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [54, 55, 56, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 57, 58, 59, 60]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623633463 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633463 Building ZINC001623633464 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623633464 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/160 `/scratch/xiaobo/369383/xbb-8058088.28/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]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001623633464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623633464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623633464 none CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 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, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 49, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [54, 55, 56, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 57, 58, 59, 60]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/161 `/scratch/xiaobo/369383/xbb-8058088.28/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]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001623633464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623633464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623633464 none CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 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, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 38, 48, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [54, 55, 56, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 57, 58, 59, 60]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623633464 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 Building ZINC001623633464 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623633464 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 160) grep: /scratch/xiaobo/369383/xbb-8058088.28/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]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001623633464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623633464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623633464 none CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 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, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 49, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [54, 55, 56, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 57, 58, 59, 60]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 161) grep: /scratch/xiaobo/369383/xbb-8058088.28/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]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001623633464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623633464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623633464 none CC(C)(C)OC(=O)NC[C@H]1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 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, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 38, 48, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [54, 55, 56, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 57, 58, 59, 60]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623633464 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623633464 Building ZINC001623689213 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623689213 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/162 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/162' -> `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])c1ccc2c(c1)CCC2) `ZINC001623689213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623689213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001623689213 none O=C(Nc1cc(F)c(Cl)cc1I)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 6, 25, 25, 12, 12, 12, 12, 12, 12, 12, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/163 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/163' -> `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])c1ccc2c(c1)CCC2) `ZINC001623689213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623689213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001623689213 none O=C(Nc1cc(F)c(Cl)cc1I)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 6, 26, 26, 12, 12, 12, 12, 12, 12, 12, 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, 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/369383/xbb-8058088.28/working/building/ZINC001623689213 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623689213 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213 Building ZINC001623689213 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623689213 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 162) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cc(F)c(Cl)cc1I)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001623689213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623689213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001623689213 none O=C(Nc1cc(F)c(Cl)cc1I)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 6, 25, 25, 12, 12, 12, 12, 12, 12, 12, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 163) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cc(F)c(Cl)cc1I)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001623689213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623689213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001623689213 none O=C(Nc1cc(F)c(Cl)cc1I)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 18, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 6, 26, 26, 12, 12, 12, 12, 12, 12, 12, 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, 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/369383/xbb-8058088.28/working/building/ZINC001623689213 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623689213 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623689213 Building ZINC001623865498 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623865498 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/164 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/164' -> `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])c1ccc(Br)s1) `ZINC001623865498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623865498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623865498 none O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 9, 20, 24, 24, 21, 24, 24, 9, 14, 18, 18, 18, 20, 20, 18, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 20, 20, 24, 24, 20, 24, 24, 14, 14, 54, 20, 20, 18, 20, 20, 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: 217 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/165 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/165' -> `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])c1ccc(Br)s1) `ZINC001623865498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623865498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623865498 none O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 15, 19, 19, 16, 19, 19, 8, 13, 22, 22, 22, 23, 23, 22, 23, 23, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 19, 19, 19, 19, 19, 13, 13, 66, 23, 23, 22, 23, 23, 4, 4] 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: 221 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623865498 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 Building ZINC001623865498 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623865498 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 164) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623865498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623865498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623865498 none O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 9, 20, 24, 24, 21, 24, 24, 9, 14, 18, 18, 18, 20, 20, 18, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 20, 20, 24, 24, 20, 24, 24, 14, 14, 54, 20, 20, 18, 20, 20, 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: 217 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 165) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623865498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623865498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623865498 none O=C(N(Cc1ccccc1)C[C@H](O)c1ccccc1)[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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 15, 19, 19, 16, 19, 19, 8, 13, 22, 22, 22, 23, 23, 22, 23, 23, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 19, 19, 19, 19, 19, 13, 13, 66, 23, 23, 22, 23, 23, 4, 4] 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: 221 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623865498 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865498 Building ZINC001623865499 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623865499 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/166 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/166' -> `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])c1ccc(Br)s1) `ZINC001623865499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623865499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623865499 none O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 15, 19, 19, 17, 19, 19, 8, 13, 22, 22, 22, 23, 23, 22, 23, 23, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 19, 19, 19, 19, 19, 13, 13, 66, 23, 23, 22, 23, 23, 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: 217 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/167 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/167' -> `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])c1ccc(Br)s1) `ZINC001623865499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623865499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623865499 none O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 9, 20, 25, 25, 23, 25, 25, 9, 15, 19, 19, 19, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 25, 25, 25, 25, 25, 15, 15, 57, 21, 21, 19, 21, 21, 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: 225 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623865499 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 Building ZINC001623865499 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623865499 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 166) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623865499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623865499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623865499 none O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 15, 19, 19, 17, 19, 19, 8, 13, 22, 22, 22, 23, 23, 22, 23, 23, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 19, 19, 19, 19, 19, 13, 13, 66, 23, 23, 22, 23, 23, 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: 217 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 167) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001623865499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623865499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001623865499 none O=C(N(Cc1ccccc1)C[C@@H](O)c1ccccc1)[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.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.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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens 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, 9, 20, 25, 25, 23, 25, 25, 9, 15, 19, 19, 19, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 25, 25, 25, 25, 25, 15, 15, 57, 21, 21, 19, 21, 21, 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: 225 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623865499 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623865499 Building ZINC001623881704 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623881704 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/168 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCOCC2)c2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001623881704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623881704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623881704 none O=C(N1CC2(CCOCC2)c2ccc(Br)cc21)[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.3', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/169 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCOCC2)c2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001623881704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623881704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623881704 none O=C(N1CC2(CCOCC2)c2ccc(Br)cc21)[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.3', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 4, 4, 1, 1, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4] 30 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623881704 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 Building ZINC001623881704 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623881704 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 168) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CC2(CCOCC2)c2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001623881704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623881704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623881704 none O=C(N1CC2(CCOCC2)c2ccc(Br)cc21)[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.3', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 169) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CC2(CCOCC2)c2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001623881704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623881704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001623881704 none O=C(N1CC2(CCOCC2)c2ccc(Br)cc21)[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.3', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 4, 4, 1, 1, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4] 30 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623881704 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623881704 Building ZINC001623921087 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623921087 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/170 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/171 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/172 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/172' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/173 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/173' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623921087 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 Building ZINC001623921087 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623921087 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 170) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 171) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 172) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 173) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623921087 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 Building ZINC001623921087 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623921087 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 170) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 171) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 172) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 173) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623921087 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 Building ZINC001623921087 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623921087 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 170) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 171) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 172) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 173) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1) `ZINC001623921087.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623921087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623921087 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623921087 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623921087 Building ZINC001623925277 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623925277 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/174 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2, 2, 2, 2, 1, 2, 2, 1, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/175 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 2, 2, 2, 2, 1, 2, 2, 1, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/176 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/176' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 4, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/177 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/177' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 4, 4, 4, 4, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623925277 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 Building ZINC001623925277 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623925277 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 174) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2, 2, 2, 2, 1, 2, 2, 1, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 175) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 2, 2, 2, 2, 1, 2, 2, 1, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 176) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 4, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 177) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 4, 4, 4, 4, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623925277 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 Building ZINC001623925277 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623925277 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 174) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2, 2, 2, 2, 1, 2, 2, 1, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 175) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 2, 2, 2, 2, 1, 2, 2, 1, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 176) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 4, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 177) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 4, 4, 4, 4, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623925277 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 Building ZINC001623925277 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001623925277 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 174) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2, 2, 2, 2, 1, 2, 2, 1, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 175) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 4, 4, 4, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 2, 2, 2, 2, 1, 2, 2, 1, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 176) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 4, 4, 4, 4, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 177) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1) `ZINC001623925277.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001623925277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001623925277 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc([N@]3CC[N@@](CCc4ccccc4)CC3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 4, 4, 4, 4, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623925277 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623925277 Building ZINC001623968865 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623968865 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/178 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623968865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623968865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001623968865 none CCOCCOc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 27, 15, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 30, 30, 27, 27, 6, 6, 6, 3, 4, 4, 4, 4] 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: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/179 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623968865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623968865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001623968865 none CCOCCOc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 31, 28, 15, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 31, 31, 28, 28, 6, 6, 6, 3, 4, 4, 4, 4] 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623968865 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 Building ZINC001623968865 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623968865 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 178) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOCCOc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623968865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623968865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001623968865 none CCOCCOc1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 27, 15, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 30, 30, 27, 27, 6, 6, 6, 3, 4, 4, 4, 4] 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: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 179) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOCCOc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001623968865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623968865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001623968865 none CCOCCOc1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 31, 28, 15, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 31, 31, 28, 28, 6, 6, 6, 3, 4, 4, 4, 4] 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623968865 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623968865 Building ZINC001623975960 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623975960 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/180 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCc2c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cccc2C1) `ZINC001623975960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623975960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001623975960 none CC(C)(C)OC(=O)N1CCc2c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cccc2C1 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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 30, 46, 30, 30, 30, 23, 10, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 3, 2, 2, 2, 2, 30, 30, 30, 30, 30] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/181 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCc2c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cccc2C1) `ZINC001623975960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623975960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001623975960 none CC(C)(C)OC(=O)N1CCc2c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cccc2C1 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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 31, 48, 31, 31, 31, 24, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 11, 11, 3, 2, 2, 2, 2, 31, 31, 31, 31, 31] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623975960 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 Building ZINC001623975960 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001623975960 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 180) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCc2c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cccc2C1) `ZINC001623975960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001623975960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001623975960 none CC(C)(C)OC(=O)N1CCc2c(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cccc2C1 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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 30, 46, 30, 30, 30, 23, 10, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 3, 2, 2, 2, 2, 30, 30, 30, 30, 30] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 181) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCc2c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cccc2C1) `ZINC001623975960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001623975960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001623975960 none CC(C)(C)OC(=O)N1CCc2c(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cccc2C1 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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 31, 48, 31, 31, 31, 24, 11, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 11, 11, 3, 2, 2, 2, 2, 31, 31, 31, 31, 31] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001623975960 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001623975960 Building ZINC001624023415 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624023415 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/182 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624023415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023415 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [26, 24, 9, 24, 24, 24, 24, 24, 24, 24, 24, 3, 9, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 24, 24, 24, 24, 9, 9, 9, 3, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/183 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624023415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023415 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [30, 26, 11, 26, 26, 26, 26, 26, 26, 26, 26, 4, 11, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 26, 26, 26, 26, 11, 11, 11, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624023415 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 Building ZINC001624023415 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624023415 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 182) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624023415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023415 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [26, 24, 9, 24, 24, 24, 24, 24, 24, 24, 24, 3, 9, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 24, 24, 24, 24, 9, 9, 9, 3, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 183) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624023415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023415 none CO[C@@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [30, 26, 11, 26, 26, 26, 26, 26, 26, 26, 26, 4, 11, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 26, 26, 26, 26, 11, 11, 11, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624023415 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023415 Building ZINC001624023416 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624023416 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/184 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624023416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023416 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [31, 26, 15, 26, 26, 26, 26, 26, 26, 26, 26, 4, 15, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 31, 31, 31, 26, 26, 26, 26, 15, 15, 15, 4, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/185 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624023416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023416 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [28, 26, 17, 26, 26, 26, 26, 26, 26, 26, 26, 5, 17, 17, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 28, 28, 28, 26, 26, 26, 26, 17, 17, 17, 5, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624023416 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 Building ZINC001624023416 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624023416 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 184) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624023416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023416 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [31, 26, 15, 26, 26, 26, 26, 26, 26, 26, 26, 4, 15, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 31, 31, 31, 26, 26, 26, 26, 15, 15, 15, 4, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 185) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624023416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023416 none CO[C@@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [28, 26, 17, 26, 26, 26, 26, 26, 26, 26, 26, 5, 17, 17, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 28, 28, 28, 26, 26, 26, 26, 17, 17, 17, 5, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624023416 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023416 Building ZINC001624023417 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624023417 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/186 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624023417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023417 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [28, 26, 17, 26, 26, 26, 26, 26, 26, 26, 26, 5, 17, 17, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 28, 28, 28, 26, 26, 26, 26, 17, 17, 17, 5, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/187 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624023417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023417 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [31, 26, 15, 26, 26, 26, 26, 26, 26, 26, 26, 4, 15, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 31, 31, 31, 26, 26, 26, 26, 15, 15, 15, 4, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624023417 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 Building ZINC001624023417 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624023417 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 186) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624023417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023417 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [28, 26, 17, 26, 26, 26, 26, 26, 26, 26, 26, 5, 17, 17, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 28, 28, 28, 26, 26, 26, 26, 17, 17, 17, 5, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 187) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624023417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023417 none CO[C@H](c1ccc(Br)cc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [31, 26, 15, 26, 26, 26, 26, 26, 26, 26, 26, 4, 15, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 31, 31, 31, 26, 26, 26, 26, 15, 15, 15, 4, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624023417 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023417 Building ZINC001624023418 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624023418 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/188 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624023418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023418 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [29, 25, 11, 25, 25, 25, 25, 25, 25, 25, 25, 4, 11, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 25, 25, 25, 25, 11, 11, 11, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/189 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624023418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023418 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [26, 24, 9, 24, 24, 24, 24, 24, 24, 24, 24, 3, 9, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 24, 24, 24, 24, 9, 9, 9, 3, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624023418 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 Building ZINC001624023418 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624023418 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 188) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624023418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023418 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [29, 25, 11, 25, 25, 25, 25, 25, 25, 25, 25, 4, 11, 11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 25, 25, 25, 25, 11, 11, 11, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 189) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624023418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624023418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624023418 none CO[C@H](c1ccc(Br)cc1)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [26, 24, 9, 24, 24, 24, 24, 24, 24, 24, 24, 3, 9, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 24, 24, 24, 24, 9, 9, 9, 3, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624023418 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624023418 Building ZINC001624136617 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624136617 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/190 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [27, 27, 27, 27, 23, 27, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 5, 5, 5, 5, 27, 27, 27, 27] 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/191 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [30, 30, 30, 30, 23, 30, 7, 7, 7, 3, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 6, 7, 3, 4, 4, 4, 4, 30, 30, 30, 30] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/192 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/192' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [27, 27, 27, 27, 24, 27, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 4, 4, 4, 4, 27, 27, 27, 27] 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/193 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/193' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [26, 26, 26, 26, 23, 26, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 3, 4, 4, 4, 4, 26, 26, 26, 26] 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624136617 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 Building ZINC001624136617 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624136617 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 190) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [27, 27, 27, 27, 23, 27, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 5, 5, 5, 5, 27, 27, 27, 27] 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 191) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [30, 30, 30, 30, 23, 30, 7, 7, 7, 3, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 6, 7, 3, 4, 4, 4, 4, 30, 30, 30, 30] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 192) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [27, 27, 27, 27, 24, 27, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 4, 4, 4, 4, 27, 27, 27, 27] 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 193) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [26, 26, 26, 26, 23, 26, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 3, 4, 4, 4, 4, 26, 26, 26, 26] 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624136617 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 Building ZINC001624136617 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624136617 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 190) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [27, 27, 27, 27, 23, 27, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 5, 5, 5, 5, 27, 27, 27, 27] 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 191) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [30, 30, 30, 30, 23, 30, 7, 7, 7, 3, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 6, 7, 3, 4, 4, 4, 4, 30, 30, 30, 30] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 192) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [27, 27, 27, 27, 24, 27, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 4, 4, 4, 4, 27, 27, 27, 27] 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 193) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [26, 26, 26, 26, 23, 26, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 3, 4, 4, 4, 4, 26, 26, 26, 26] 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624136617 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 Building ZINC001624136617 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624136617 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 190) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [27, 27, 27, 27, 23, 27, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 5, 5, 5, 5, 27, 27, 27, 27] 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 191) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [30, 30, 30, 30, 23, 30, 7, 7, 7, 3, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 6, 7, 3, 4, 4, 4, 4, 30, 30, 30, 30] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 192) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [27, 27, 27, 27, 24, 27, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 3, 4, 4, 4, 4, 27, 27, 27, 27] 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: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 193) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001624136617.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624136617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624136617 none C[N@]1CC[C@@H](Oc2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', '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', '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, 10, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [26, 26, 26, 26, 23, 26, 6, 6, 6, 3, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 3, 4, 4, 4, 4, 26, 26, 26, 26] 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624136617 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624136617 Building ZINC001624152445 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624152445 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/194 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001624152445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624152445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001624152445 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 10, 10, 10, 10, 20, 20, 20, 38, 38, 50, 50, 50, 50, 20, 20, 20, 20, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 134 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/195 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001624152445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624152445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001624152445 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 11, 11, 11, 11, 20, 20, 20, 39, 39, 50, 50, 50, 50, 20, 20, 20, 20, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 136 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624152445 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 Building ZINC001624152445 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624152445 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 194) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001624152445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624152445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001624152445 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 10, 10, 10, 10, 20, 20, 20, 38, 38, 50, 50, 50, 50, 20, 20, 20, 20, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 134 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 195) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001624152445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624152445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001624152445 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 11, 11, 11, 11, 20, 20, 20, 39, 39, 50, 50, 50, 50, 20, 20, 20, 20, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 136 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624152445 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152445 Building ZINC001624152446 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624152446 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/196 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001624152446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624152446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001624152446 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 9, 9, 9, 9, 20, 20, 20, 42, 42, 50, 50, 50, 50, 20, 20, 20, 20, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 144 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/197 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001624152446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624152446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001624152446 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 9, 9, 9, 9, 17, 17, 17, 39, 39, 50, 50, 50, 50, 17, 17, 17, 17, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 140 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624152446 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 Building ZINC001624152446 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624152446 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 196) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001624152446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624152446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001624152446 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 9, 9, 9, 9, 20, 20, 20, 42, 42, 50, 50, 50, 50, 20, 20, 20, 20, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 144 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 197) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001624152446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624152446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001624152446 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 9, 9, 9, 9, 17, 17, 17, 39, 39, 50, 50, 50, 50, 17, 17, 17, 17, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 140 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624152446 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624152446 Building ZINC001624154117 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624154117 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/198 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(C)(C)[C@@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001624154117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624154117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624154117 none CC(C)(C)OC(=O)N1CC(C)(C)[C@@H]1C1CCN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 13, 26, 13, 13, 13, 13, 13, 8, 13, 8, 8, 8, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 5, 5, 8, 8, 8, 8] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/199 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(C)(C)[C@@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001624154117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624154117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624154117 none CC(C)(C)OC(=O)N1CC(C)(C)[C@@H]1C1CCN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 17, 28, 17, 17, 17, 17, 17, 10, 17, 10, 10, 10, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10, 5, 5, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624154117 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 Building ZINC001624154117 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624154117 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 198) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC(C)(C)[C@@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001624154117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624154117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624154117 none CC(C)(C)OC(=O)N1CC(C)(C)[C@@H]1C1CCN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 13, 26, 13, 13, 13, 13, 13, 8, 13, 8, 8, 8, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 5, 5, 8, 8, 8, 8] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 199) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC(C)(C)[C@@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001624154117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624154117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624154117 none CC(C)(C)OC(=O)N1CC(C)(C)[C@@H]1C1CCN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 17, 28, 17, 17, 17, 17, 17, 10, 17, 10, 10, 10, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10, 5, 5, 10, 10, 10, 10] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624154117 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154117 Building ZINC001624154120 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624154120 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/200 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(C)(C)[C@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001624154120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624154120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624154120 none CC(C)(C)OC(=O)N1CC(C)(C)[C@H]1C1CCN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 21, 12, 21, 12, 12, 12, 12, 12, 9, 12, 9, 9, 9, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/201 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC(C)(C)[C@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001624154120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624154120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624154120 none CC(C)(C)OC(=O)N1CC(C)(C)[C@H]1C1CCN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 12, 23, 12, 12, 12, 12, 12, 10, 12, 10, 10, 10, 4, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 3, 3, 10, 10, 10, 10] 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: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624154120 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 Building ZINC001624154120 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624154120 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 200) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC(C)(C)[C@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001624154120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624154120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624154120 none CC(C)(C)OC(=O)N1CC(C)(C)[C@H]1C1CCN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 21, 12, 21, 12, 12, 12, 12, 12, 9, 12, 9, 9, 9, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 201) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC(C)(C)[C@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001624154120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624154120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624154120 none CC(C)(C)OC(=O)N1CC(C)(C)[C@H]1C1CCN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 12, 23, 12, 12, 12, 12, 12, 10, 12, 10, 10, 10, 4, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 3, 3, 10, 10, 10, 10] 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: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624154120 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624154120 Building ZINC001624196016 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624196016 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/202 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(Cl)cc3)cc2)c1) `ZINC001624196016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624196016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001624196016 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(Cl)cc3)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.ar', 'C.ar', 'C.ar', '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.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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 5, 6, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 6, 6, 4, 4, 4, 4, 2, 4, 4, 3, 6, 6, 26, 26, 26, 26, 26, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/203 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(Cl)cc3)cc2)c1) `ZINC001624196016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624196016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001624196016 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(Cl)cc3)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.ar', 'C.ar', 'C.ar', '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.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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 3, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 6, 6, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 26, 26, 26, 26, 26, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624196016 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 Building ZINC001624196016 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624196016 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 202) grep: /scratch/xiaobo/369383/xbb-8058088.28/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([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(Cl)cc3)cc2)c1) `ZINC001624196016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624196016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001624196016 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(Cl)cc3)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.ar', 'C.ar', 'C.ar', '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.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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 5, 6, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 6, 6, 4, 4, 4, 4, 2, 4, 4, 3, 6, 6, 26, 26, 26, 26, 26, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 203) grep: /scratch/xiaobo/369383/xbb-8058088.28/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([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(Cl)cc3)cc2)c1) `ZINC001624196016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624196016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001624196016 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(S(=O)(=O)Nc3ccc(Cl)cc3)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.ar', 'C.ar', 'C.ar', '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.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, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 3, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 6, 6, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 26, 26, 26, 26, 26, 6, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624196016 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624196016 Building ZINC001624313646 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624313646 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/204 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1) `ZINC001624313646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624313646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001624313646 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1 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', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 2, 2, 6, 6, 6, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/205 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1) `ZINC001624313646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624313646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001624313646 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1 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', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 2, 4, 6, 6, 6, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624313646 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 Building ZINC001624313646 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624313646 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 204) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1) `ZINC001624313646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624313646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001624313646 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1 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', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 2, 2, 6, 6, 6, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 205) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1) `ZINC001624313646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624313646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001624313646 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(OC)c(S(=O)(=O)Nc2ccc(Cl)cc2)c1 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', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 2, 4, 6, 6, 6, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624313646 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624313646 Building ZINC001624372167 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624372167 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/206 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCO2) `ZINC001624372167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624372167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001624372167 none CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCO2 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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 12, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 36, 25, 36, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 25, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/207 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCO2) `ZINC001624372167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624372167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001624372167 none CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCO2 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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 12, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 25, 36, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624372167 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 Building ZINC001624372167 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624372167 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 206) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCO2) `ZINC001624372167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624372167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001624372167 none CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)CCO2 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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 12, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 36, 25, 36, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 25, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 207) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCO2) `ZINC001624372167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624372167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001624372167 none CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)CCO2 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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 12, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 25, 36, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624372167 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624372167 Building ZINC001624376461 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624376461 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/208 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)OC(C)(C)C) `ZINC001624376461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624376461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001624376461 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)OC(C)(C)C 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 20, 24, 24, 27, 27, 27, 27, 26, 26, 26, 13, 13, 3, 4, 4, 4, 4, 13, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/209 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)OC(C)(C)C) `ZINC001624376461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624376461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001624376461 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)OC(C)(C)C 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 18, 22, 22, 26, 26, 26, 26, 23, 23, 23, 11, 11, 3, 4, 4, 4, 4, 11, 18, 26, 26, 26, 26, 26, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624376461 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 Building ZINC001624376461 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624376461 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 208) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)OC(C)(C)C) `ZINC001624376461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624376461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001624376461 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)OC(C)(C)C 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 20, 24, 24, 27, 27, 27, 27, 26, 26, 26, 13, 13, 3, 4, 4, 4, 4, 13, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 209) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)OC(C)(C)C) `ZINC001624376461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624376461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC001624376461 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)OC(C)(C)C 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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 18, 22, 22, 26, 26, 26, 26, 23, 23, 23, 11, 11, 3, 4, 4, 4, 4, 11, 18, 26, 26, 26, 26, 26, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624376461 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624376461 Building ZINC001624444265 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624444265 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/210 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624444265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624444265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624444265 none C[C@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', '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, 1, 1, 1, 1, 15, 1, 16, 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, 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, 7, 7] 0 hydrogens need 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, 16, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 3, 1, 4, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 8, 8, 8, 16, 16, 28, 28, 28, 8, 8, 8, 8, 8, 8, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/211 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624444265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624444265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624444265 none C[C@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', '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, 1, 1, 1, 1, 15, 1, 16, 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, 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, 7, 7] 0 hydrogens 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, 15, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 4, 1, 5, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 9, 9, 9, 15, 15, 28, 28, 28, 9, 9, 9, 9, 9, 9, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624444265 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 Building ZINC001624444265 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624444265 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 210) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624444265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624444265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624444265 none C[C@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', '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, 1, 1, 1, 1, 15, 1, 16, 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, 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, 7, 7] 0 hydrogens need 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, 16, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 3, 1, 4, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 8, 8, 8, 16, 16, 28, 28, 28, 8, 8, 8, 8, 8, 8, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 211) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624444265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624444265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624444265 none C[C@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', '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, 1, 1, 1, 1, 15, 1, 16, 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, 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, 7, 7] 0 hydrogens 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, 15, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 4, 1, 5, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 9, 9, 9, 15, 15, 28, 28, 28, 9, 9, 9, 9, 9, 9, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624444265 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444265 Building ZINC001624444266 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624444266 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/212 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624444266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624444266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624444266 none C[C@@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', '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, 1, 1, 1, 1, 15, 1, 16, 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, 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, 7, 7] 0 hydrogens 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, 15, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 4, 1, 5, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 9, 9, 9, 15, 15, 28, 28, 28, 9, 9, 9, 9, 9, 9, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/213 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624444266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624444266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624444266 none C[C@@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', '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, 1, 1, 1, 1, 15, 1, 16, 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, 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, 7, 7] 0 hydrogens need 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, 16, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 3, 1, 4, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 8, 8, 8, 16, 16, 28, 28, 28, 8, 8, 8, 8, 8, 8, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624444266 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 Building ZINC001624444266 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624444266 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 212) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624444266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624444266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624444266 none C[C@@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', '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, 1, 1, 1, 1, 15, 1, 16, 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, 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, 7, 7] 0 hydrogens 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, 15, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 4, 1, 5, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 9, 9, 9, 15, 15, 28, 28, 28, 9, 9, 9, 9, 9, 9, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 213) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001624444266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624444266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624444266 none C[C@@]1(Cc2ccc(F)c(Cl)c2)CCCN1C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', '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, 1, 1, 1, 1, 15, 1, 16, 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, 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, 7, 7] 0 hydrogens need 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, 16, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 3, 1, 4, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 8, 8, 8, 16, 16, 28, 28, 28, 8, 8, 8, 8, 8, 8, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624444266 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624444266 Building ZINC001624445477 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624445477 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/214 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1c(F)cccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624445477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624445477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624445477 none O=C(NC[C@@H](c1c(F)cccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 22, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 34, 34, 34, 34, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 22, 22, 33, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 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: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/215 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1c(F)cccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624445477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624445477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624445477 none O=C(NC[C@@H](c1c(F)cccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 20, 20, 31, 31, 31, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624445477 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 Building ZINC001624445477 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624445477 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 214) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@@H](c1c(F)cccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624445477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624445477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624445477 none O=C(NC[C@@H](c1c(F)cccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 22, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 34, 34, 34, 34, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 22, 22, 33, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 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: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 215) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@@H](c1c(F)cccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624445477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624445477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624445477 none O=C(NC[C@@H](c1c(F)cccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 20, 20, 31, 31, 31, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624445477 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445477 Building ZINC001624445478 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624445478 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/216 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1c(F)cccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624445478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624445478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624445478 none O=C(NC[C@H](c1c(F)cccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 21, 21, 31, 31, 31, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/217 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1c(F)cccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624445478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624445478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624445478 none O=C(NC[C@H](c1c(F)cccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 22, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 35, 35, 35, 35, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 22, 22, 33, 33, 33, 35, 35, 35, 35, 35, 35, 35, 35, 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624445478 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 Building ZINC001624445478 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624445478 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 216) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@H](c1c(F)cccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624445478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624445478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624445478 none O=C(NC[C@H](c1c(F)cccc1Cl)N1CCCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 21, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 36, 36, 36, 36, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 21, 21, 31, 31, 31, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 217) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@H](c1c(F)cccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624445478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624445478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624445478 none O=C(NC[C@H](c1c(F)cccc1Cl)N1CCCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 15, 1, 1, 1, 1, 16, 10, 5, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 22, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 35, 35, 35, 35, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 22, 22, 33, 33, 33, 35, 35, 35, 35, 35, 35, 35, 35, 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624445478 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624445478 Building ZINC001624492829 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624492829 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/218 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/218' -> `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]1CCC12CCOCC2) `ZINC001624492829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624492829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624492829 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 5, 5, 5, 5, 2, 2, 2, 2, 6, 6, 16, 16, 16, 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, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/219 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/219' -> `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]1CCC12CCOCC2) `ZINC001624492829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624492829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624492829 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624492829 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 Building ZINC001624492829 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624492829 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 218) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC12CCOCC2) `ZINC001624492829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624492829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624492829 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 5, 5, 5, 5, 2, 2, 2, 2, 6, 6, 16, 16, 16, 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, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 219) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC12CCOCC2) `ZINC001624492829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624492829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624492829 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624492829 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492829 Building ZINC001624492830 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624492830 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/220 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/220' -> `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]1CCC12CCOCC2) `ZINC001624492830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624492830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624492830 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 8, 8, 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, 57]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/221 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/221' -> `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]1CCC12CCOCC2) `ZINC001624492830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624492830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624492830 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 18, 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, 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/369383/xbb-8058088.28/working/building/ZINC001624492830 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624492830 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830 Building ZINC001624492830 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624492830 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 220) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC12CCOCC2) `ZINC001624492830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624492830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624492830 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 8, 8, 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, 57]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 221) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC12CCOCC2) `ZINC001624492830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624492830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001624492830 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 18, 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, 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/369383/xbb-8058088.28/working/building/ZINC001624492830 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624492830 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624492830 Building ZINC001624595952 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624595952 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/222 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1n1cnc2ccccc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001624595952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624595952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624595952 none O=C(NCc1cccnc1n1cnc2ccccc21)[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', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', '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, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 27, 27, 27, 50, 50, 50, 50, 50, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/223 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccnc1n1cnc2ccccc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001624595952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624595952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624595952 none O=C(NCc1cccnc1n1cnc2ccccc21)[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', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', '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, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 28, 28, 28, 50, 50, 50, 50, 50, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624595952 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 Building ZINC001624595952 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624595952 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 222) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NCc1cccnc1n1cnc2ccccc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001624595952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624595952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624595952 none O=C(NCc1cccnc1n1cnc2ccccc21)[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', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', '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, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 27, 27, 27, 50, 50, 50, 50, 50, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 223) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NCc1cccnc1n1cnc2ccccc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001624595952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624595952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001624595952 none O=C(NCc1cccnc1n1cnc2ccccc21)[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', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', '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, 5, 1, 1, 1, 1, 8, 1, 8, 1, 8, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 28, 28, 28, 50, 50, 50, 50, 50, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624595952 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624595952 Building ZINC001624658002 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624658002 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/224 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 16, 16, 16, 16, 31, 32, 32, 31, 31, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 31, 31, 32, 32, 32, 32, 16, 16, 16, 16, 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/225 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 16, 16, 16, 16, 31, 32, 32, 31, 31, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 31, 31, 32, 32, 32, 32, 16, 16, 16, 16, 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/226 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/226' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 15, 15, 15, 15, 31, 33, 33, 31, 31, 33, 33, 33, 33, 33, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 31, 31, 33, 33, 33, 33, 15, 15, 15, 15, 5, 5, 5, 5] 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/227 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/227' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 15, 15, 15, 15, 31, 33, 33, 31, 31, 33, 33, 33, 33, 33, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 31, 31, 33, 33, 33, 33, 15, 15, 15, 15, 5, 5, 5, 5] 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624658002 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 Building ZINC001624658002 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624658002 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 224) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 16, 16, 16, 16, 31, 32, 32, 31, 31, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 31, 31, 32, 32, 32, 32, 16, 16, 16, 16, 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 225) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 16, 16, 16, 16, 31, 32, 32, 31, 31, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 31, 31, 32, 32, 32, 32, 16, 16, 16, 16, 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 226) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 15, 15, 15, 15, 31, 33, 33, 31, 31, 33, 33, 33, 33, 33, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 31, 31, 33, 33, 33, 33, 15, 15, 15, 15, 5, 5, 5, 5] 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 227) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 15, 15, 15, 15, 31, 33, 33, 31, 31, 33, 33, 33, 33, 33, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 31, 31, 33, 33, 33, 33, 15, 15, 15, 15, 5, 5, 5, 5] 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624658002 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 Building ZINC001624658002 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624658002 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 224) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 16, 16, 16, 16, 31, 32, 32, 31, 31, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 31, 31, 32, 32, 32, 32, 16, 16, 16, 16, 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 225) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 16, 16, 16, 16, 31, 32, 32, 31, 31, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 31, 31, 32, 32, 32, 32, 16, 16, 16, 16, 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 226) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 15, 15, 15, 15, 31, 33, 33, 31, 31, 33, 33, 33, 33, 33, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 31, 31, 33, 33, 33, 33, 15, 15, 15, 15, 5, 5, 5, 5] 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 227) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 15, 15, 15, 15, 31, 33, 33, 31, 31, 33, 33, 33, 33, 33, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 31, 31, 33, 33, 33, 33, 15, 15, 15, 15, 5, 5, 5, 5] 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624658002 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 Building ZINC001624658002 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001624658002 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 224) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 16, 16, 16, 16, 31, 32, 32, 31, 31, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 31, 31, 32, 32, 32, 32, 16, 16, 16, 16, 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 225) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 16, 16, 16, 16, 31, 32, 32, 31, 31, 32, 32, 32, 32, 32, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 31, 31, 32, 32, 32, 32, 16, 16, 16, 16, 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 226) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 15, 15, 15, 15, 31, 33, 33, 31, 31, 33, 33, 33, 33, 33, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 31, 31, 33, 33, 33, 33, 15, 15, 15, 15, 5, 5, 5, 5] 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 227) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001624658002.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001624658002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001624658002 none O=C(N1CCCN(Cc2ccc(C(F)(F)F)cc2)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.3', 'N.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', 'O.3', 'C.2', 'C.2', 'N.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, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 15, 15, 15, 15, 15, 31, 33, 33, 31, 31, 33, 33, 33, 33, 33, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 31, 31, 33, 33, 33, 33, 15, 15, 15, 15, 5, 5, 5, 5] 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624658002 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624658002 Building ZINC001624670047 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624670047 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/228 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(OC)c(OC)c1) `ZINC001624670047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624670047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001624670047 none CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 1, 12, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 19, 19, 19, 19, 34, 19, 19, 36, 19, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 3, 4, 4, 4, 4, 19, 19, 34, 34, 34, 36, 36, 36, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/229 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(OC)c(OC)c1) `ZINC001624670047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624670047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001624670047 none CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 1, 12, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 19, 19, 19, 19, 34, 19, 19, 36, 19, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 3, 4, 4, 4, 4, 19, 19, 34, 34, 34, 36, 36, 36, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624670047 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 Building ZINC001624670047 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624670047 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 228) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(OC)c(OC)c1) `ZINC001624670047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624670047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001624670047 none CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 1, 12, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 19, 19, 19, 19, 34, 19, 19, 36, 19, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 3, 4, 4, 4, 4, 19, 19, 34, 34, 34, 36, 36, 36, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 229) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(OC)c(OC)c1) `ZINC001624670047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624670047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001624670047 none CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 1, 12, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 19, 19, 19, 19, 34, 19, 19, 36, 19, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 3, 4, 4, 4, 4, 19, 19, 34, 34, 34, 36, 36, 36, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624670047 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624670047 Building ZINC001624731066 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624731066 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/230 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1) `ZINC001624731066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624731066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001624731066 none COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 18, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 22, 22, 14, 22, 22, 22, 19, 19, 19, 18, 18, 3, 3, 1, 3, 22, 22, 22, 22] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 146 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/231 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1) `ZINC001624731066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624731066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001624731066 none COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 17, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 25, 25, 16, 25, 25, 25, 20, 20, 20, 17, 17, 4, 3, 1, 3, 25, 25, 25, 25] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 146 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624731066 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 Building ZINC001624731066 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624731066 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 230) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1) `ZINC001624731066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624731066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001624731066 none COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 18, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 22, 22, 14, 22, 22, 22, 19, 19, 19, 18, 18, 3, 3, 1, 3, 22, 22, 22, 22] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 146 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 231) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1) `ZINC001624731066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624731066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001624731066 none COC[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 17, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 25, 25, 16, 25, 25, 25, 20, 20, 20, 17, 17, 4, 3, 1, 3, 25, 25, 25, 25] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 146 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624731066 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731066 Building ZINC001624731067 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624731067 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/232 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1) `ZINC001624731067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624731067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001624731067 none COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 18, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 25, 25, 16, 25, 25, 25, 21, 21, 21, 18, 18, 4, 3, 1, 3, 25, 25, 17, 25] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/233 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1) `ZINC001624731067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624731067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001624731067 none COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 18, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 22, 22, 14, 22, 22, 22, 19, 19, 19, 18, 18, 3, 3, 1, 3, 22, 22, 14, 22] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624731067 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 Building ZINC001624731067 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001624731067 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 232) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1) `ZINC001624731067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001624731067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001624731067 none COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 18, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 25, 25, 16, 25, 25, 25, 21, 21, 21, 18, 18, 4, 3, 1, 3, 25, 25, 17, 25] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 233) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1) `ZINC001624731067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001624731067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001624731067 none COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 18, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 22, 22, 14, 22, 22, 22, 19, 19, 19, 18, 18, 3, 3, 1, 3, 22, 22, 14, 22] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001624731067 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001624731067 Building ZINC001625011456 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625011456 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/234 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1ccccc1)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1F) `ZINC001625011456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625011456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625011456 none O=C(Cc1ccccc1)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 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: [12, 12, 12, 29, 29, 29, 29, 29, 29, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 12, 8, 3, 3, 3, 3, 3, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/235 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1ccccc1)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1F) `ZINC001625011456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625011456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625011456 none O=C(Cc1ccccc1)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 30, 30, 30, 30, 30, 30, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 13, 8, 3, 4, 4, 4, 4, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625011456 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 Building ZINC001625011456 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625011456 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 234) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Cc1ccccc1)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1F) `ZINC001625011456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625011456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625011456 none O=C(Cc1ccccc1)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 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: [12, 12, 12, 29, 29, 29, 29, 29, 29, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 12, 8, 3, 3, 3, 3, 3, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 235) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Cc1ccccc1)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1F) `ZINC001625011456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625011456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625011456 none O=C(Cc1ccccc1)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 30, 30, 30, 30, 30, 30, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 13, 8, 3, 4, 4, 4, 4, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625011456 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625011456 Building ZINC001625083651 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625083651 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/236 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(Cl)cc(Br)c2)cc1Cl) `ZINC001625083651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625083651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001625083651 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(Cl)cc(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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 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] 0 hydrogens 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, 8, 11, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 9, 9, 9, 4, 4, 2, 8, 8, 11, 11, 22, 22, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/237 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(Cl)cc(Br)c2)cc1Cl) `ZINC001625083651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625083651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001625083651 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(Cl)cc(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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 11, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 9, 9, 9, 4, 4, 2, 8, 8, 11, 11, 22, 22, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625083651 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 Building ZINC001625083651 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625083651 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 236) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(Cl)cc(Br)c2)cc1Cl) `ZINC001625083651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625083651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001625083651 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(Cl)cc(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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 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] 0 hydrogens 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, 8, 11, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 9, 9, 9, 4, 4, 2, 8, 8, 11, 11, 22, 22, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 237) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(Cl)cc(Br)c2)cc1Cl) `ZINC001625083651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625083651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001625083651 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(Cl)cc(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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 11, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 9, 9, 9, 4, 4, 2, 8, 8, 11, 11, 22, 22, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625083651 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625083651 Building ZINC001625150523 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625150523 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/238 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(F)c(F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 50, 50, 50, 12, 12, 12, 12, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/239 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 50, 50, 50, 12, 12, 12, 12, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/240 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/240' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(F)c(F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 48, 48, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 48, 48, 48, 12, 12, 12, 12, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/241 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/241' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 48, 48, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 48, 48, 48, 12, 12, 12, 12, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625150523 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 Building ZINC001625150523 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625150523 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 238) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@](Cc2ccc(F)c(F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 50, 50, 50, 12, 12, 12, 12, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 239) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@@](Cc2ccc(F)c(F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 50, 50, 50, 12, 12, 12, 12, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 240) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(F)c(F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 48, 48, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 48, 48, 48, 12, 12, 12, 12, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 241) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 48, 48, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 48, 48, 48, 12, 12, 12, 12, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625150523 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 Building ZINC001625150523 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625150523 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 238) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@](Cc2ccc(F)c(F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 50, 50, 50, 12, 12, 12, 12, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 239) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@@](Cc2ccc(F)c(F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 50, 50, 50, 12, 12, 12, 12, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 240) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(F)c(F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 48, 48, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 48, 48, 48, 12, 12, 12, 12, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 241) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 48, 48, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 48, 48, 48, 12, 12, 12, 12, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625150523 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 Building ZINC001625150523 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625150523 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 238) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@](Cc2ccc(F)c(F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 50, 50, 50, 12, 12, 12, 12, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 239) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@@](Cc2ccc(F)c(F)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 12, 12, 12, 12, 25, 25, 50, 50, 50, 12, 12, 12, 12, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 240) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(F)c(F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 48, 48, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 48, 48, 48, 12, 12, 12, 12, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 241) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(F)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625150523.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625150523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625150523 none O=C(N[C@H]1CC[N@@](Cc2ccc(F)c(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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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] 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] 0 hydrogens need rotated 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, 12, 12, 12, 12, 12, 25, 48, 48, 48, 48, 48, 48, 48, 12, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 12, 12, 12, 12, 25, 25, 48, 48, 48, 12, 12, 12, 12, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625150523 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625150523 Building ZINC001625272459 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625272459 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/242 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/242' -> `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]1c1cccc(C(F)(F)F)c1) `ZINC001625272459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625272459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625272459 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 11, 11, 11, 11, 11, 37, 37, 21, 37, 37, 37, 37, 37, 37, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 11, 11, 37, 37, 37, 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, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/243 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/243' -> `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]1c1cccc(C(F)(F)F)c1) `ZINC001625272459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625272459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625272459 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 38, 38, 21, 38, 38, 38, 38, 38, 38, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 10, 10, 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625272459 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 Building ZINC001625272459 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625272459 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 242) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1cccc(C(F)(F)F)c1) `ZINC001625272459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625272459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625272459 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 11, 11, 11, 11, 11, 37, 37, 21, 37, 37, 37, 37, 37, 37, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 11, 11, 37, 37, 37, 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, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 243) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1cccc(C(F)(F)F)c1) `ZINC001625272459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625272459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625272459 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 38, 38, 21, 38, 38, 38, 38, 38, 38, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 10, 10, 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625272459 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625272459 Building ZINC001625313189 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625313189 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/244 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/244' -> `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[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 11, 20, 20, 20, 20, 20, 20, 20, 22, 32, 32, 22, 32, 32, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 32, 32, 22, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 129 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/245 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/245' -> `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[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 11, 19, 19, 19, 19, 19, 19, 19, 25, 35, 35, 25, 35, 35, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 25, 25, 35, 35, 25, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/246 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/246' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 11, 20, 20, 20, 20, 20, 20, 20, 22, 32, 32, 22, 32, 32, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 32, 32, 22, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 129 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/247 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/247' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 11, 19, 19, 19, 19, 19, 19, 19, 25, 35, 35, 25, 35, 35, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 25, 25, 35, 35, 25, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625313189 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 Building ZINC001625313189 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625313189 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 244) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 11, 20, 20, 20, 20, 20, 20, 20, 22, 32, 32, 22, 32, 32, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 32, 32, 22, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 129 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 245) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 11, 19, 19, 19, 19, 19, 19, 19, 25, 35, 35, 25, 35, 35, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 25, 25, 35, 35, 25, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 246) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 11, 20, 20, 20, 20, 20, 20, 20, 22, 32, 32, 22, 32, 32, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 32, 32, 22, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 129 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 247) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 11, 19, 19, 19, 19, 19, 19, 19, 25, 35, 35, 25, 35, 35, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 25, 25, 35, 35, 25, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625313189 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 Building ZINC001625313189 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625313189 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 244) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 11, 20, 20, 20, 20, 20, 20, 20, 22, 32, 32, 22, 32, 32, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 32, 32, 22, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 129 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 245) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 11, 19, 19, 19, 19, 19, 19, 19, 25, 35, 35, 25, 35, 35, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 25, 25, 35, 35, 25, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 246) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 11, 20, 20, 20, 20, 20, 20, 20, 22, 32, 32, 22, 32, 32, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 32, 32, 22, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 129 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 247) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 11, 19, 19, 19, 19, 19, 19, 19, 25, 35, 35, 25, 35, 35, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 25, 25, 35, 35, 25, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625313189 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 Building ZINC001625313189 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625313189 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 244) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 11, 20, 20, 20, 20, 20, 20, 20, 22, 32, 32, 22, 32, 32, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 32, 32, 22, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 129 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 245) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 11, 19, 19, 19, 19, 19, 19, 19, 25, 35, 35, 25, 35, 35, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 25, 25, 35, 35, 25, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 246) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 11, 20, 20, 20, 20, 20, 20, 20, 22, 32, 32, 22, 32, 32, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 32, 32, 22, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 129 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 247) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@@H]1CCCCN1Cc1ccccc1) `ZINC001625313189.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625313189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001625313189 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 11, 19, 19, 19, 19, 19, 19, 19, 25, 35, 35, 25, 35, 35, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 25, 25, 35, 35, 25, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625313189 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625313189 Building ZINC001625338008 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625338008 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/248 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625338008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625338008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625338008 none CC(C)(C)OC(=O)NCCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 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, 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] 0 hydrogens need rotated 50 conformations 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, 28, 42, 14, 14, 9, 5, 9, 11, 11, 11, 11, 1, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 14, 14, 14, 14, 11, 11, 2, 1, 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]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/249 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625338008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625338008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625338008 none CC(C)(C)OC(=O)NCCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 27, 41, 13, 13, 8, 4, 8, 10, 10, 10, 10, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 13, 13, 13, 13, 10, 10, 3, 1, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625338008 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 Building ZINC001625338008 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625338008 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 248) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625338008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625338008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625338008 none CC(C)(C)OC(=O)NCCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 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, 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] 0 hydrogens need rotated 50 conformations 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, 28, 42, 14, 14, 9, 5, 9, 11, 11, 11, 11, 1, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 14, 14, 14, 14, 11, 11, 2, 1, 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]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 249) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001625338008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625338008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001625338008 none CC(C)(C)OC(=O)NCCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 27, 41, 13, 13, 8, 4, 8, 10, 10, 10, 10, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 13, 13, 13, 13, 10, 10, 3, 1, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625338008 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625338008 Building ZINC001625340056 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625340056 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/250 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C1) `ZINC001625340056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625340056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001625340056 none CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 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, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 31, 26, 31, 26, 26, 26, 26, 26, 26, 14, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 26, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 4, 7, 7, 26, 26, 26] 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/251 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C1) `ZINC001625340056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625340056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001625340056 none CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 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, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 32, 27, 32, 27, 27, 27, 27, 27, 27, 15, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 15, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 34, 27, 27, 27, 27, 27, 27, 4, 5, 5, 27, 27, 27] 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625340056 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 Building ZINC001625340056 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625340056 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 250) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C1) `ZINC001625340056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625340056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001625340056 none CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 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, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 31, 26, 31, 26, 26, 26, 26, 26, 26, 14, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 26, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 4, 7, 7, 26, 26, 26] 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 251) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C1) `ZINC001625340056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625340056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001625340056 none CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 5, 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, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 32, 27, 32, 27, 27, 27, 27, 27, 27, 15, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 15, 27, 27, 34, 34, 34, 34, 34, 34, 34, 34, 34, 27, 27, 27, 27, 27, 27, 4, 5, 5, 27, 27, 27] 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: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625340056 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625340056 Building ZINC001625424993 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625424993 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/252 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625424993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625424993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625424993 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[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', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 32, 32, 32, 18, 32, 32, 32, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 32, 31, 32, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/253 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625424993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625424993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625424993 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[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', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 32, 32, 32, 13, 32, 32, 32, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 32, 17, 32, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625424993 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 Building ZINC001625424993 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625424993 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 252) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625424993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625424993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625424993 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[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', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 18, 32, 32, 32, 18, 32, 32, 32, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 32, 31, 32, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 253) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625424993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625424993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625424993 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@H]1CCCN1C(=O)[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', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 32, 32, 32, 13, 32, 32, 32, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 32, 17, 32, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625424993 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424993 Building ZINC001625424994 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625424994 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/254 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625424994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625424994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625424994 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[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', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/255 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625424994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625424994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625424994 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[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', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 19, 19, 32, 32, 32, 19, 32, 32, 32, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 32, 31, 32, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/369383/xbb-8058088.28/working/building/ZINC001625424994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625424994 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994 Building ZINC001625424994 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625424994 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 254) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625424994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625424994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625424994 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[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', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 255) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001625424994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625424994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625424994 none O=C(Nc1cc(Cl)cc(Cl)c1)[C@@H]1CCCN1C(=O)[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', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 19, 19, 32, 32, 32, 19, 32, 32, 32, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 32, 31, 32, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/369383/xbb-8058088.28/working/building/ZINC001625424994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625424994 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625424994 Building ZINC001625469308 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625469308 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/256 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c1ccccc1)c1ccccc1Br) `ZINC001625469308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625469308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001625469308 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c1ccccc1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 30, 30, 38, 38, 38, 38, 38, 30, 40, 40, 33, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 38, 38, 38, 38, 38, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/257 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](c1ccccc1)c1ccccc1Br) `ZINC001625469308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625469308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001625469308 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](c1ccccc1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 36, 36, 43, 43, 40, 43, 43, 36, 44, 44, 39, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 43, 43, 36, 43, 43, 44, 44, 39, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625469308 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 Building ZINC001625469308 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625469308 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 256) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c1ccccc1)c1ccccc1Br) `ZINC001625469308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625469308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001625469308 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c1ccccc1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 30, 30, 38, 38, 38, 38, 38, 30, 40, 40, 33, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 38, 38, 38, 38, 38, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 257) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](c1ccccc1)c1ccccc1Br) `ZINC001625469308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625469308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001625469308 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](c1ccccc1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 36, 36, 43, 43, 40, 43, 43, 36, 44, 44, 39, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 43, 43, 36, 43, 43, 44, 44, 39, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625469308 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469308 Building ZINC001625469309 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625469309 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/258 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](c1ccccc1)c1ccccc1Br) `ZINC001625469309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625469309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001625469309 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](c1ccccc1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 36, 36, 43, 43, 36, 43, 43, 36, 44, 44, 39, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 43, 43, 43, 43, 43, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/259 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](c1ccccc1)c1ccccc1Br) `ZINC001625469309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625469309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001625469309 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](c1ccccc1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 30, 30, 38, 38, 30, 38, 38, 30, 40, 40, 30, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 38, 38, 30, 38, 38, 40, 40, 33, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625469309 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 Building ZINC001625469309 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625469309 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 258) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](c1ccccc1)c1ccccc1Br) `ZINC001625469309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625469309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001625469309 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](c1ccccc1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 36, 36, 43, 43, 36, 43, 43, 36, 44, 44, 39, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 43, 43, 43, 43, 43, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 259) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](c1ccccc1)c1ccccc1Br) `ZINC001625469309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625469309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001625469309 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](c1ccccc1)c1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 30, 30, 38, 38, 30, 38, 38, 30, 40, 40, 30, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 38, 38, 30, 38, 38, 40, 40, 33, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625469309 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625469309 Building ZINC001625479283 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625479283 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/260 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@@H](O)c2ccc(Br)cc2)C1) `ZINC001625479283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625479283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479283 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 10, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 16, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 144, 48, 48, 48, 48, 16, 16] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 309 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/261 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@@H](O)c2ccc(Br)cc2)C1) `ZINC001625479283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625479283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479283 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 9, 18, 18, 18, 18, 18, 18, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 147, 49, 49, 49, 49, 18, 18] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 324 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625479283 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 Building ZINC001625479283 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625479283 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 260) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@@H](O)c2ccc(Br)cc2)C1) `ZINC001625479283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625479283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479283 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 10, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 16, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 144, 48, 48, 48, 48, 16, 16] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 309 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 261) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@@H](O)c2ccc(Br)cc2)C1) `ZINC001625479283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625479283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479283 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 9, 18, 18, 18, 18, 18, 18, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 147, 49, 49, 49, 49, 18, 18] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 324 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625479283 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479283 Building ZINC001625479284 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625479284 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/262 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@H](O)c2ccc(Br)cc2)C1) `ZINC001625479284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625479284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479284 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 11, 17, 17, 17, 17, 17, 17, 48, 48, 48, 48, 48, 48, 48, 48, 48, 17, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 144, 48, 48, 48, 48, 17, 17] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 302 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/263 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@H](O)c2ccc(Br)cc2)C1) `ZINC001625479284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625479284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479284 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 9, 15, 15, 15, 15, 15, 15, 49, 49, 49, 49, 49, 49, 49, 49, 49, 15, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 147, 49, 49, 49, 49, 15, 15] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625479284 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 Building ZINC001625479284 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625479284 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 262) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@H](O)c2ccc(Br)cc2)C1) `ZINC001625479284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625479284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479284 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 11, 17, 17, 17, 17, 17, 17, 48, 48, 48, 48, 48, 48, 48, 48, 48, 17, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 144, 48, 48, 48, 48, 17, 17] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 302 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 263) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@H](O)c2ccc(Br)cc2)C1) `ZINC001625479284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625479284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479284 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]([C@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 9, 15, 15, 15, 15, 15, 15, 49, 49, 49, 49, 49, 49, 49, 49, 49, 15, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 147, 49, 49, 49, 49, 15, 15] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625479284 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479284 Building ZINC001625479285 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625479285 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/264 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H](O)c2ccc(Br)cc2)C1) `ZINC001625479285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625479285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479285 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 10, 19, 19, 19, 19, 19, 19, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 144, 48, 48, 48, 48, 19, 19] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 310 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/265 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H](O)c2ccc(Br)cc2)C1) `ZINC001625479285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625479285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479285 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 12, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 47, 47, 19, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 141, 47, 47, 47, 47, 19, 19] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 296 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625479285 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 Building ZINC001625479285 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625479285 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 264) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H](O)c2ccc(Br)cc2)C1) `ZINC001625479285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625479285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479285 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 10, 19, 19, 19, 19, 19, 19, 48, 48, 48, 48, 48, 48, 48, 48, 48, 19, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 144, 48, 48, 48, 48, 19, 19] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 310 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 265) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H](O)c2ccc(Br)cc2)C1) `ZINC001625479285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625479285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479285 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 7, 12, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 47, 47, 19, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 141, 47, 47, 47, 47, 19, 19] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 296 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625479285 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479285 Building ZINC001625479286 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625479286 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/266 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H](O)c2ccc(Br)cc2)C1) `ZINC001625479286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625479286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479286 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 10, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 16, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 144, 48, 48, 48, 48, 16, 16] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 308 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/267 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H](O)c2ccc(Br)cc2)C1) `ZINC001625479286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625479286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479286 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 11, 17, 17, 17, 17, 17, 17, 48, 48, 48, 48, 48, 48, 48, 48, 48, 17, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 144, 48, 48, 48, 48, 17, 17] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 302 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625479286 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 Building ZINC001625479286 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625479286 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 266) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H](O)c2ccc(Br)cc2)C1) `ZINC001625479286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625479286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479286 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 10, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 16, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 144, 48, 48, 48, 48, 16, 16] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 308 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 267) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H](O)c2ccc(Br)cc2)C1) `ZINC001625479286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625479286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001625479286 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H](O)c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 12, 1, 1, 1, 1, 17, 1, 1, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 11, 17, 17, 17, 17, 17, 17, 48, 48, 48, 48, 48, 48, 48, 48, 48, 17, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 144, 48, 48, 48, 48, 17, 17] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 302 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625479286 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625479286 Building ZINC001625568624 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625568624 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/268 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/268' -> `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]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001625568624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625568624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001625568624 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 45, 45, 50, 50, 50, 50, 32, 32, 2, 2, 2, 2, 2, 2, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/269 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/269' -> `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]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001625568624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625568624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001625568624 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 35, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2, 2, 2, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625568624 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 Building ZINC001625568624 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625568624 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 268) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001625568624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625568624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001625568624 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 45, 45, 50, 50, 50, 50, 32, 32, 2, 2, 2, 2, 2, 2, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 269) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001625568624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625568624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001625568624 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 35, 35, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2, 2, 2, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625568624 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568624 Building ZINC001625568626 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625568626 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/270 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/270' -> `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]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001625568626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625568626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001625568626 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 33, 33, 48, 48, 48, 48, 22, 22, 2, 2, 2, 2, 2, 2, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 48, 48, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/271 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/271' -> `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]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001625568626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625568626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001625568626 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 33, 33, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625568626 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 Building ZINC001625568626 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625568626 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 270) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001625568626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625568626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001625568626 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 33, 33, 48, 48, 48, 48, 22, 22, 2, 2, 2, 2, 2, 2, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 48, 48, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 271) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001625568626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625568626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001625568626 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCCC12CCN(C(=O)OC(C)(C)C)CC2 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.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 33, 33, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625568626 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625568626 Building ZINC001625573412 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625573412 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/272 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCCCCNC(=O)OC(C)(C)C)cc1Cl) `ZINC001625573412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625573412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001625573412 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCCCCNC(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 4, 5, 5, 5, 5, 11, 23, 32, 32, 32, 32, 32, 32, 2, 2, 2, 4, 4, 4, 2, 2, 2, 2, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 23, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/273 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCCNC(=O)OC(C)(C)C)cc1Cl) `ZINC001625573412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625573412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001625573412 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCCNC(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 10, 22, 31, 31, 31, 31, 31, 31, 2, 2, 2, 5, 5, 5, 2, 2, 2, 2, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 22, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625573412 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 Building ZINC001625573412 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625573412 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 272) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCCCCNC(=O)OC(C)(C)C)cc1Cl) `ZINC001625573412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625573412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001625573412 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)CCCCCCNC(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 4, 5, 5, 5, 5, 11, 23, 32, 32, 32, 32, 32, 32, 2, 2, 2, 4, 4, 4, 2, 2, 2, 2, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 23, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 273) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCCNC(=O)OC(C)(C)C)cc1Cl) `ZINC001625573412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625573412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001625573412 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCCNC(=O)OC(C)(C)C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 10, 22, 31, 31, 31, 31, 31, 31, 2, 2, 2, 5, 5, 5, 2, 2, 2, 2, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 22, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625573412 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625573412 Building ZINC001625577921 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625577921 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/274 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 22, 13, 22, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 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/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/275 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 22, 13, 22, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 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/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/276 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/276' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 8, 8, 20, 19, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/277 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/277' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 8, 8, 20, 19, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625577921 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 Building ZINC001625577921 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625577921 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 274) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 22, 13, 22, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 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/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 275) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 22, 13, 22, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 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/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 276) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 8, 8, 20, 19, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 277) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 8, 8, 20, 19, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625577921 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 Building ZINC001625577921 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625577921 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 274) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 22, 13, 22, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 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/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 275) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 22, 13, 22, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 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/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 276) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 8, 8, 20, 19, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 277) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 8, 8, 20, 19, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625577921 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 Building ZINC001625577921 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625577921 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 274) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 22, 13, 22, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 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/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 275) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 22, 13, 22, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 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/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 276) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 8, 8, 20, 19, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 277) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577921.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625577921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577921 none C[C@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 8, 8, 20, 19, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625577921 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577921 Building ZINC001625577922 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625577922 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/278 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 8, 8, 20, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/279 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 8, 8, 20, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/280 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/280' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 40, 13, 13, 22, 21, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/281 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/281' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 40, 13, 13, 22, 21, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625577922 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 Building ZINC001625577922 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625577922 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 278) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 8, 8, 20, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 279) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 8, 8, 20, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 280) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 40, 13, 13, 22, 21, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 281) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 40, 13, 13, 22, 21, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625577922 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 Building ZINC001625577922 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625577922 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 278) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 8, 8, 20, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 279) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 8, 8, 20, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 280) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 40, 13, 13, 22, 21, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 281) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 40, 13, 13, 22, 21, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625577922 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 Building ZINC001625577922 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625577922 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 278) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 8, 8, 20, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 279) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 8, 8, 20, 20, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 8, 8, 2, 2, 2, 20, 20, 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, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 280) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 40, 13, 13, 22, 21, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 281) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1) `ZINC001625577922.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625577922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001625577922 none C[C@@H]1CCCN(Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 40, 13, 13, 22, 21, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 22, 22, 8, 8, 2, 2, 2, 22, 22, 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, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625577922 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625577922 Building ZINC001625611543 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625611543 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/282 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC001625611543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625611543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611543 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 8, 8, 8, 8, 4, 2, 3, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 8, 23, 23, 23, 23, 23, 12, 12, 12, 12, 8, 8, 8, 8, 8, 8, 6, 6, 14, 14, 14, 6, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/283 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC001625611543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625611543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611543 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9, 9, 9, 9, 6, 2, 4, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 9, 22, 22, 22, 22, 22, 12, 12, 12, 12, 9, 9, 9, 9, 9, 9, 6, 6, 12, 12, 12, 6, 9, 9] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625611543 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 Building ZINC001625611543 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625611543 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 282) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC001625611543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625611543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611543 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 8, 8, 8, 8, 4, 2, 3, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 8, 23, 23, 23, 23, 23, 12, 12, 12, 12, 8, 8, 8, 8, 8, 8, 6, 6, 14, 14, 14, 6, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 283) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC001625611543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625611543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611543 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 9, 9, 9, 9, 6, 2, 4, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 9, 22, 22, 22, 22, 22, 12, 12, 12, 12, 9, 9, 9, 9, 9, 9, 6, 6, 12, 12, 12, 6, 9, 9] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625611543 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611543 Building ZINC001625611544 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625611544 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/284 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC001625611544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625611544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611544 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 10, 10, 10, 10, 10, 6, 2, 4, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 10, 23, 23, 23, 23, 23, 14, 14, 14, 14, 10, 10, 10, 10, 10, 10, 6, 6, 12, 12, 12, 6, 10, 10] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/285 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC001625611544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625611544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611544 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 4, 2, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 9, 24, 24, 24, 24, 24, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 6, 6, 13, 13, 13, 6, 9, 9] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625611544 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 Building ZINC001625611544 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625611544 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 284) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC001625611544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625611544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611544 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 10, 10, 10, 10, 10, 6, 2, 4, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 10, 23, 23, 23, 23, 23, 14, 14, 14, 14, 10, 10, 10, 10, 10, 10, 6, 6, 12, 12, 12, 6, 10, 10] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 285) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC001625611544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625611544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611544 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 4, 2, 3, 1, 1, 1, 6, 6, 2, 6, 13, 6, 6, 6, 9, 24, 24, 24, 24, 24, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 6, 6, 13, 13, 13, 6, 9, 9] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625611544 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611544 Building ZINC001625611820 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625611820 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/286 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001625611820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625611820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611820 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 7, 2, 5, 1, 1, 1, 7, 7, 7, 7, 7, 12, 32, 32, 32, 32, 32, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 7, 7, 12, 12] 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]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/287 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001625611820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625611820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611820 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 6, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 11, 30, 30, 30, 30, 30, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 6, 6, 11, 11] 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]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625611820 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 Building ZINC001625611820 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625611820 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 286) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001625611820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625611820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611820 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 7, 2, 5, 1, 1, 1, 7, 7, 7, 7, 7, 12, 32, 32, 32, 32, 32, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 7, 7, 12, 12] 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]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 287) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001625611820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625611820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611820 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 6, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 11, 30, 30, 30, 30, 30, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 6, 6, 11, 11] 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]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625611820 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611820 Building ZINC001625611821 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625611821 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/288 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001625611821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625611821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611821 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 5, 2, 4, 1, 1, 1, 7, 7, 7, 7, 7, 9, 31, 31, 31, 31, 31, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 7, 7, 9, 9] 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]) total number of confs: 97 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/289 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001625611821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625611821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611821 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 7, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 11, 33, 33, 33, 33, 33, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 6, 6, 11, 11] 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]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625611821 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 Building ZINC001625611821 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001625611821 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 288) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001625611821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625611821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611821 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 5, 2, 4, 1, 1, 1, 7, 7, 7, 7, 7, 9, 31, 31, 31, 31, 31, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 7, 7, 9, 9] 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]) total number of confs: 97 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 289) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001625611821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625611821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001625611821 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 7, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 11, 33, 33, 33, 33, 33, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 6, 6, 11, 11] 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]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625611821 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625611821 Building ZINC001625736753 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625736753 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/290 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 16, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 3, 3, 3, 3, 3, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/291 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 40, 38, 40, 40, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/292 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/292' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 16, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 3, 3, 3, 3, 3, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/293 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/293' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 40, 38, 40, 40, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625736753 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 Building ZINC001625736753 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625736753 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 290) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 16, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 3, 3, 3, 3, 3, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 291) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 40, 38, 40, 40, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 292) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 16, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 3, 3, 3, 3, 3, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 293) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 40, 38, 40, 40, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625736753 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 Building ZINC001625736753 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625736753 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 290) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 16, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 3, 3, 3, 3, 3, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 291) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 40, 38, 40, 40, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 292) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 16, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 3, 3, 3, 3, 3, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 293) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 40, 38, 40, 40, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625736753 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 Building ZINC001625736753 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625736753 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 290) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 16, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 3, 3, 3, 3, 3, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 291) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 40, 38, 40, 40, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 292) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 25, 16, 25, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 44, 44, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 3, 3, 3, 3, 3, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 293) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736753.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625736753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736753 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 40, 38, 40, 40, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625736753 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736753 Building ZINC001625736754 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625736754 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/294 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 38, 38, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 16, 16, 4, 4, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/295 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 24, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/296 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/296' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 38, 38, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 16, 16, 4, 4, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/297 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/297' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 24, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625736754 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 Building ZINC001625736754 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625736754 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 294) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 38, 38, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 16, 16, 4, 4, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 295) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 24, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 296) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 38, 38, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 16, 16, 4, 4, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 297) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 24, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625736754 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 Building ZINC001625736754 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625736754 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 294) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 38, 38, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 16, 16, 4, 4, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 295) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 24, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 296) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 38, 38, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 16, 16, 4, 4, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 297) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 24, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625736754 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 Building ZINC001625736754 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001625736754 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 294) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 38, 38, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 16, 16, 4, 4, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 295) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 24, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 296) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 38, 38, 30, 16, 30, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 34, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 16, 16, 4, 4, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 38, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 297) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1) `ZINC001625736754.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001625736754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001625736754 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cccn2C)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 24, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 29, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 3, 3, 3, 3, 3, 3, 3, 43, 43, 43, 43, 43, 43, 43, 43, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001625736754 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001625736754 Building ZINC001626296056 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626296056 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/298 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)c1ccc(F)cc1) `ZINC001626296056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626296056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001626296056 none O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 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, 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: [34, 34, 29, 29, 29, 29, 29, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 34, 38, 38, 34, 38, 38, 38, 34, 29, 29, 29, 16, 16, 3, 4, 4, 4, 4, 29, 38, 38, 38, 38] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/299 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)c1ccc(F)cc1) `ZINC001626296056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626296056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001626296056 none O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 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, 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: [34, 34, 29, 29, 29, 29, 29, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 34, 41, 41, 34, 41, 41, 41, 34, 29, 29, 29, 16, 16, 3, 4, 4, 4, 4, 29, 41, 41, 41, 41] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626296056 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 Building ZINC001626296056 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626296056 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 298) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)c1ccc(F)cc1) `ZINC001626296056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626296056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001626296056 none O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 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, 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: [34, 34, 29, 29, 29, 29, 29, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 34, 38, 38, 34, 38, 38, 38, 34, 29, 29, 29, 16, 16, 3, 4, 4, 4, 4, 29, 38, 38, 38, 38] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 299) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)c1ccc(F)cc1) `ZINC001626296056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626296056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001626296056 none O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 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, 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: [34, 34, 29, 29, 29, 29, 29, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 34, 41, 41, 34, 41, 41, 41, 34, 29, 29, 29, 16, 16, 3, 4, 4, 4, 4, 29, 41, 41, 41, 41] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626296056 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626296056 Building ZINC001626349686 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626349686 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/300 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1CCN2C(=O)C(F)(F)F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626349686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626349686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001626349686 none O=C(Nc1cccc2c1CCN2C(=O)C(F)(F)F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 7, 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: [6, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 27, 27, 27, 27, 27, 27, 27, 5, 2, 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]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/301 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1CCN2C(=O)C(F)(F)F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626349686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626349686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001626349686 none O=C(Nc1cccc2c1CCN2C(=O)C(F)(F)F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 7, 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: [6, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 27, 27, 27, 27, 27, 27, 27, 5, 1, 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]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626349686 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 Building ZINC001626349686 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626349686 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 300) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cccc2c1CCN2C(=O)C(F)(F)F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626349686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626349686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001626349686 none O=C(Nc1cccc2c1CCN2C(=O)C(F)(F)F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 7, 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: [6, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 27, 27, 27, 27, 27, 27, 27, 5, 2, 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]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 301) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cccc2c1CCN2C(=O)C(F)(F)F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626349686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626349686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001626349686 none O=C(Nc1cccc2c1CCN2C(=O)C(F)(F)F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 7, 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: [6, 1, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 27, 27, 27, 27, 27, 27, 27, 5, 1, 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]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626349686 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626349686 Building ZINC001626386901 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626386901 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/302 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001626386901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626386901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626386901 none O=C(Nc1ccccc1)Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 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.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 37, 39, 39, 37, 39, 39, 19, 19, 19, 19, 19, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 37, 39, 39, 39, 39, 39, 33, 19, 19, 19, 7, 7, 2, 2, 2, 2, 2, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/303 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001626386901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626386901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626386901 none O=C(Nc1ccccc1)Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 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.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 38, 39, 39, 39, 39, 39, 18, 18, 18, 18, 18, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 38, 39, 39, 39, 39, 39, 34, 18, 18, 18, 7, 7, 2, 2, 2, 2, 2, 18] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626386901 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 Building ZINC001626386901 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626386901 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 302) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccccc1)Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001626386901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626386901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626386901 none O=C(Nc1ccccc1)Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 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.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 37, 39, 39, 37, 39, 39, 19, 19, 19, 19, 19, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 37, 39, 39, 39, 39, 39, 33, 19, 19, 19, 7, 7, 2, 2, 2, 2, 2, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 303) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccccc1)Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001626386901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626386901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626386901 none O=C(Nc1ccccc1)Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 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.am', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 38, 39, 39, 39, 39, 39, 18, 18, 18, 18, 18, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 38, 39, 39, 39, 39, 39, 34, 18, 18, 18, 7, 7, 2, 2, 2, 2, 2, 18] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626386901 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626386901 Building ZINC001626470565 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626470565 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/304 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cnn1c1cc(F)c(OC)cc1F) `ZINC001626470565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626470565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001626470565 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cnn1c1cc(F)c(OC)cc1F 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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 15, 1, 12, 5, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 41, 41, 41, 41, 41, 46, 41, 41, 41, 18, 18, 18, 18, 18, 16, 16, 4, 2, 2, 2, 2, 2, 2, 8, 41, 46, 46, 46, 41] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/305 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cnn1c1cc(F)c(OC)cc1F) `ZINC001626470565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626470565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001626470565 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cnn1c1cc(F)c(OC)cc1F 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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 15, 1, 12, 5, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 41, 41, 41, 40, 41, 46, 41, 41, 41, 18, 18, 18, 18, 18, 16, 16, 4, 2, 2, 2, 2, 2, 2, 8, 41, 46, 46, 46, 41] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626470565 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 Building ZINC001626470565 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626470565 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 304) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cnn1c1cc(F)c(OC)cc1F) `ZINC001626470565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626470565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001626470565 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)cnn1c1cc(F)c(OC)cc1F 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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 15, 1, 12, 5, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 41, 41, 41, 41, 41, 46, 41, 41, 41, 18, 18, 18, 18, 18, 16, 16, 4, 2, 2, 2, 2, 2, 2, 8, 41, 46, 46, 46, 41] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 305) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cnn1c1cc(F)c(OC)cc1F) `ZINC001626470565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626470565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001626470565 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)cnn1c1cc(F)c(OC)cc1F 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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 8, 1, 1, 1, 15, 1, 12, 5, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 41, 41, 41, 40, 41, 46, 41, 41, 41, 18, 18, 18, 18, 18, 16, 16, 4, 2, 2, 2, 2, 2, 2, 8, 41, 46, 46, 46, 41] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626470565 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626470565 Building ZINC001626572096 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626572096 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/306 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1) `ZINC001626572096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626572096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626572096 none CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 5, 8, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 5, 17, 17, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 3, 6, 6, 2, 6, 6, 6, 6, 17, 17, 17] 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: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/307 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1) `ZINC001626572096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626572096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626572096 none CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 17, 17, 12, 17, 17, 17, 17, 15, 15, 15, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17] 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626572096 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 Building ZINC001626572096 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626572096 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 306) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1) `ZINC001626572096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626572096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626572096 none CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 5, 8, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 5, 17, 17, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 3, 6, 6, 2, 6, 6, 6, 6, 17, 17, 17] 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: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 307) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1) `ZINC001626572096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626572096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626572096 none CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 17, 17, 12, 17, 17, 17, 17, 15, 15, 15, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17] 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626572096 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572096 Building ZINC001626572097 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626572097 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/308 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1) `ZINC001626572097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626572097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626572097 none CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 17, 17, 14, 17, 17, 17, 17, 15, 15, 15, 15, 15, 3, 6, 6, 2, 6, 6, 6, 6, 17, 17, 17] 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/309 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1) `ZINC001626572097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626572097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626572097 none CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 5, 8, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 5, 17, 17, 15, 17, 17, 17, 17, 15, 15, 15, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626572097 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 Building ZINC001626572097 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626572097 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 308) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1) `ZINC001626572097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626572097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626572097 none CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 17, 17, 14, 17, 17, 17, 17, 15, 15, 15, 15, 15, 3, 6, 6, 2, 6, 6, 6, 6, 17, 17, 17] 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 309) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1) `ZINC001626572097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626572097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001626572097 none CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)c1ccc(Br)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 5, 8, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 5, 17, 17, 15, 17, 17, 17, 17, 15, 15, 15, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626572097 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626572097 Building ZINC001626654530 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001626654530 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/310 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 11, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 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, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/311 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 7, 10, 33, 33, 33, 33, 50, 50, 50, 33, 33, 7, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 7, 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, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/312 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/312' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 2, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/313 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/313' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 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, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626654530 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 Building ZINC001626654530 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001626654530 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 310) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 11, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 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, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 311) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 7, 10, 33, 33, 33, 33, 50, 50, 50, 33, 33, 7, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 7, 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, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 312) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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([N@]2CC[N@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 2, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 313) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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([N@]2CC[N@@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 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, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626654530 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 Building ZINC001626654530 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001626654530 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 310) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 11, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 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, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 311) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 7, 10, 33, 33, 33, 33, 50, 50, 50, 33, 33, 7, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 7, 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, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 312) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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([N@]2CC[N@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 2, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 313) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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([N@]2CC[N@@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 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, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626654530 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 Building ZINC001626654530 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001626654530 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 310) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 11, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 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, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 311) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 7, 10, 33, 33, 33, 33, 50, 50, 50, 33, 33, 7, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 7, 7, 7, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 7, 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, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 312) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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([N@]2CC[N@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 2, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 313) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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([N@]2CC[N@@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626654530.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001626654530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001626654530 none O=C(Nc1cccc([N@]2CC[N@@](CC3CC3)CC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 33, 33, 33, 33, 50, 50, 50, 33, 33, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 8, 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, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626654530 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626654530 Building ZINC001626666913 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626666913 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/314 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(c2ccc(F)cc2)nc2ccc(F)cn21)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626666913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626666913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001626666913 none O=C(NCc1c(c2ccc(F)cc2)nc2ccc(F)cn21)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'F', 'C.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 36, 36, 39, 39, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 39, 39, 39, 39, 36, 36, 36, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/315 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(c2ccc(F)cc2)nc2ccc(F)cn21)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626666913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626666913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001626666913 none O=C(NCc1c(c2ccc(F)cc2)nc2ccc(F)cn21)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'F', 'C.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 36, 36, 39, 39, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 39, 39, 39, 39, 36, 36, 36, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626666913 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 Building ZINC001626666913 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626666913 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 314) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(c2ccc(F)cc2)nc2ccc(F)cn21)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626666913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626666913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001626666913 none O=C(NCc1c(c2ccc(F)cc2)nc2ccc(F)cn21)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'F', 'C.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 36, 36, 39, 39, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 39, 39, 39, 39, 36, 36, 36, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 315) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(c2ccc(F)cc2)nc2ccc(F)cn21)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626666913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626666913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001626666913 none O=C(NCc1c(c2ccc(F)cc2)nc2ccc(F)cn21)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'F', 'C.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 36, 36, 39, 39, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 39, 39, 39, 39, 36, 36, 36, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626666913 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626666913 Building ZINC001626715483 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626715483 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/316 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)OC(C)(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001626715483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626715483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001626715483 none COc1ccc(NC(=O)OC(C)(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 19, 27, 27, 31, 31, 31, 31, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 4, 4, 4, 4, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/317 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)OC(C)(C)C)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001626715483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626715483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001626715483 none COc1ccc(NC(=O)OC(C)(C)C)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 18, 27, 27, 30, 30, 30, 30, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 3, 4, 4, 4, 4, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626715483 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 Building ZINC001626715483 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626715483 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 316) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(NC(=O)OC(C)(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001626715483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626715483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001626715483 none COc1ccc(NC(=O)OC(C)(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 19, 27, 27, 31, 31, 31, 31, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 4, 4, 4, 4, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 317) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(NC(=O)OC(C)(C)C)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001626715483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626715483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001626715483 none COc1ccc(NC(=O)OC(C)(C)C)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 18, 27, 27, 30, 30, 30, 30, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 3, 4, 4, 4, 4, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626715483 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626715483 Building ZINC001626730713 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626730713 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/318 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/318' -> `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)NCCCOc1ccc(Cl)cc1C) `ZINC001626730713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626730713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001626730713 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOc1ccc(Cl)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 12, 1, 1, 1, 1, 16, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 9, 14, 30, 50, 50, 35, 37, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 11, 11, 12, 12, 13, 13, 50, 50, 50, 50, 50, 50] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/319 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/319' -> `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)NCCCOc1ccc(Cl)cc1C) `ZINC001626730713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626730713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001626730713 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOc1ccc(Cl)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 12, 1, 1, 1, 1, 16, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 9, 14, 31, 50, 50, 37, 37, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 12, 12, 13, 13, 50, 50, 50, 50, 50, 50] 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: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626730713 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 Building ZINC001626730713 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626730713 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 318) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOc1ccc(Cl)cc1C) `ZINC001626730713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626730713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001626730713 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCOc1ccc(Cl)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 12, 1, 1, 1, 1, 16, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 9, 14, 30, 50, 50, 35, 37, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 11, 11, 12, 12, 13, 13, 50, 50, 50, 50, 50, 50] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 319) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOc1ccc(Cl)cc1C) `ZINC001626730713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626730713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001626730713 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCOc1ccc(Cl)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 12, 1, 1, 1, 1, 16, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 9, 14, 31, 50, 50, 37, 37, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 11, 11, 12, 12, 13, 13, 50, 50, 50, 50, 50, 50] 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: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626730713 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626730713 Building ZINC001626758897 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626758897 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/320 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626758897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626758897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626758897 none O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 13, 38, 38, 38, 38, 38, 38, 5, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 13, 38, 38, 38, 38, 5, 5, 4, 4] 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]) total number of confs: 74 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/321 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626758897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626758897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626758897 none O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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] 0 hydrogens need 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, 6, 6, 6, 6, 6, 21, 44, 44, 44, 44, 44, 44, 6, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 21, 44, 44, 44, 44, 6, 6, 2, 2] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626758897 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 Building ZINC001626758897 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626758897 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 320) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626758897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626758897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626758897 none O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 13, 38, 38, 38, 38, 38, 38, 5, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 13, 38, 38, 38, 38, 5, 5, 4, 4] 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]) total number of confs: 74 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 321) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626758897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626758897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626758897 none O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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] 0 hydrogens need 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, 6, 6, 6, 6, 6, 21, 44, 44, 44, 44, 44, 44, 6, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 21, 44, 44, 44, 44, 6, 6, 2, 2] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626758897 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758897 Building ZINC001626758898 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626758898 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/322 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626758898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626758898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626758898 none O=C(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 11, 33, 33, 30, 33, 33, 33, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 11, 33, 33, 33, 33, 4, 4, 3, 3] 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]) total number of confs: 75 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/323 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626758898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626758898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626758898 none O=C(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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] 0 hydrogens need 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, 6, 6, 6, 6, 6, 16, 38, 38, 38, 38, 38, 38, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 16, 38, 38, 38, 38, 6, 6, 4, 4] 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]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626758898 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 Building ZINC001626758898 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626758898 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 322) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626758898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626758898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626758898 none O=C(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 11, 33, 33, 30, 33, 33, 33, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 11, 33, 33, 33, 33, 4, 4, 3, 3] 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]) total number of confs: 75 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 323) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001626758898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626758898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001626758898 none O=C(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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] 0 hydrogens need 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, 6, 6, 6, 6, 6, 16, 38, 38, 38, 38, 38, 38, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 16, 38, 38, 38, 38, 6, 6, 4, 4] 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]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626758898 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626758898 Building ZINC001626903473 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626903473 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/324 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1c2ccccc2C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626903473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626903473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001626903473 none CC(C)(C)OC(=O)N[C@@H]1c2ccccc2C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 32, 43, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 15, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 32, 15, 15, 15, 15, 15, 15, 3, 3, 1, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/325 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1c2ccccc2C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626903473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626903473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001626903473 none CC(C)(C)OC(=O)N[C@@H]1c2ccccc2C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 31, 43, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 31, 15, 15, 15, 15, 15, 15, 2, 3, 1, 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626903473 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 Building ZINC001626903473 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626903473 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 324) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N[C@@H]1c2ccccc2C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626903473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626903473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001626903473 none CC(C)(C)OC(=O)N[C@@H]1c2ccccc2C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 32, 43, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 15, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 32, 15, 15, 15, 15, 15, 15, 3, 3, 1, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 325) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N[C@@H]1c2ccccc2C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001626903473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626903473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001626903473 none CC(C)(C)OC(=O)N[C@@H]1c2ccccc2C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 31, 43, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 31, 15, 15, 15, 15, 15, 15, 2, 3, 1, 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626903473 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626903473 Building ZINC001626997829 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626997829 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/326 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(Br)ccc2SC)cc1Cl) `ZINC001626997829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626997829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001626997829 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(Br)ccc2SC)cc1Cl NO_LONG_NAME dock atom 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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 14, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 17, 20, 20, 20, 17, 20, 20, 20, 28, 4, 4, 4, 7, 7, 7, 4, 4, 2, 9, 9, 17, 17, 20, 20, 20, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/327 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(Br)ccc2SC)cc1Cl) `ZINC001626997829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626997829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001626997829 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(Br)ccc2SC)cc1Cl NO_LONG_NAME dock atom 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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 14, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 17, 20, 20, 20, 17, 20, 20, 20, 28, 4, 4, 4, 7, 7, 7, 4, 4, 2, 9, 9, 17, 17, 20, 20, 20, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626997829 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 Building ZINC001626997829 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626997829 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 326) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(Br)ccc2SC)cc1Cl) `ZINC001626997829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626997829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001626997829 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cc(Br)ccc2SC)cc1Cl NO_LONG_NAME dock atom 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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 14, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 17, 20, 20, 20, 17, 20, 20, 20, 28, 4, 4, 4, 7, 7, 7, 4, 4, 2, 9, 9, 17, 17, 20, 20, 20, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 327) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(Br)ccc2SC)cc1Cl) `ZINC001626997829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626997829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001626997829 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cc(Br)ccc2SC)cc1Cl NO_LONG_NAME dock atom 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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 14, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 17, 20, 20, 20, 17, 20, 20, 20, 28, 4, 4, 4, 7, 7, 7, 4, 4, 2, 9, 9, 17, 17, 20, 20, 20, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001626997829 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001626997829 Building ZINC001627017550 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627017550 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/328 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC001627017550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627017550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001627017550 none Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 8, 8, 17, 33, 48, 48, 48, 48, 48, 48, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 2, 17, 17, 33, 48, 48, 48, 48, 48, 48, 48, 48, 48, 8, 2, 4, 4, 4, 4, 4, 4, 4, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/329 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC001627017550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627017550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001627017550 none Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 8, 8, 18, 33, 48, 48, 48, 48, 48, 48, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 2, 18, 18, 33, 48, 48, 48, 48, 48, 48, 48, 48, 48, 8, 2, 3, 3, 3, 3, 3, 3, 3, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627017550 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 Building ZINC001627017550 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627017550 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 328) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC001627017550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627017550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001627017550 none Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 8, 8, 17, 33, 48, 48, 48, 48, 48, 48, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 2, 17, 17, 33, 48, 48, 48, 48, 48, 48, 48, 48, 48, 8, 2, 4, 4, 4, 4, 4, 4, 4, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 329) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1) `ZINC001627017550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627017550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001627017550 none Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 8, 8, 18, 33, 48, 48, 48, 48, 48, 48, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 2, 18, 18, 33, 48, 48, 48, 48, 48, 48, 48, 48, 48, 8, 2, 3, 3, 3, 3, 3, 3, 3, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627017550 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627017550 Building ZINC001627019059 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627019059 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/330 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627019059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627019059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627019059 none O=C(N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 8, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/331 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627019059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627019059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627019059 none O=C(N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 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]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627019059 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 Building ZINC001627019059 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627019059 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 330) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627019059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627019059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627019059 none O=C(N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 8, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 331) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627019059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627019059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627019059 none O=C(N[C@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 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]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627019059 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019059 Building ZINC001627019177 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627019177 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/332 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627019177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627019177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627019177 none O=C(N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 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]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/333 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627019177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627019177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627019177 none O=C(N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 8, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627019177 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 Building ZINC001627019177 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627019177 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 332) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627019177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627019177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627019177 none O=C(N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 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]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 333) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627019177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627019177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627019177 none O=C(N[C@@]1(Cc2ccc(C(F)(F)F)cc2)CCOC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 8, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627019177 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627019177 Building ZINC001627038867 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627038867 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/334 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(O)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627038867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627038867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 29 natoms 28 natoms 27 natoms 26 names: ZINC001627038867 none O=C(Nc1c(O)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 17, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 10, 20, 20, 20, 20, 1, 1, 1, 11, 11, 11, 11, 11, 5, 40, 20, 20, 11, 11] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/335 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(O)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627038867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627038867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 29 natoms 28 natoms 27 natoms 26 names: ZINC001627038867 none O=C(Nc1c(O)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 17, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 19, 21, 21, 21, 21, 1, 1, 1, 11, 11, 11, 11, 11, 6, 42, 21, 21, 11, 11] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627038867 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 Building ZINC001627038867 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627038867 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 334) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(O)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627038867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627038867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 29 natoms 28 natoms 27 natoms 26 names: ZINC001627038867 none O=C(Nc1c(O)cc(Br)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 17, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 10, 20, 20, 20, 20, 1, 1, 1, 11, 11, 11, 11, 11, 5, 40, 20, 20, 11, 11] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 335) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(O)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627038867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627038867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 29 natoms 28 natoms 27 natoms 26 names: ZINC001627038867 none O=C(Nc1c(O)cc(Br)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 17, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 19, 21, 21, 21, 21, 1, 1, 1, 11, 11, 11, 11, 11, 6, 42, 21, 21, 11, 11] 100 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627038867 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627038867 Building ZINC001627059893 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627059893 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/336 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001627059893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627059893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001627059893 none O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 16, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 13, 13, 6, 13, 13, 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/337 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001627059893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627059893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001627059893 none O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 16, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 14, 14, 6, 14, 14, 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627059893 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 Building ZINC001627059893 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627059893 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 336) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001627059893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627059893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001627059893 none O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 16, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 13, 13, 6, 13, 13, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 13, 13, 6, 13, 13, 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 337) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001627059893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627059893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001627059893 none O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 16, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 16, 16, 16, 16, 16, 16, 16, 16, 6, 14, 14, 6, 14, 14, 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627059893 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627059893 Building ZINC001627074784 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627074784 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/338 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)S2) `ZINC001627074784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627074784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627074784 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'C.3', 'S.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, 5, 7, 5, 5, 5, 7, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/339 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)S2) `ZINC001627074784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627074784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627074784 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'C.3', 'S.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, 5, 7, 5, 5, 5, 7, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 85 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627074784 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 Building ZINC001627074784 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627074784 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 338) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)S2) `ZINC001627074784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627074784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627074784 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'C.3', 'S.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, 5, 7, 5, 5, 5, 7, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 339) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)S2) `ZINC001627074784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627074784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627074784 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'C.3', 'S.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, 5, 7, 5, 5, 5, 7, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 85 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627074784 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627074784 Building ZINC001627094331 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627094331 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/340 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627094331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094331 none CC(C)(C)OC(=O)N1CCC[C@H]1[C@@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 22, 23, 23, 18, 12, 18, 12, 12, 12, 12, 5, 12, 5, 8, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 35 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]) total number of confs: 78 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/341 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627094331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094331 none CC(C)(C)OC(=O)N1CCC[C@H]1[C@@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 32, 33, 33, 27, 14, 27, 14, 14, 14, 14, 6, 14, 6, 8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 101 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627094331 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 Building ZINC001627094331 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627094331 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 340) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@H]1[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627094331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094331 none CC(C)(C)OC(=O)N1CCC[C@H]1[C@@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 22, 23, 23, 18, 12, 18, 12, 12, 12, 12, 5, 12, 5, 8, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 35 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]) total number of confs: 78 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 341) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@H]1[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627094331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094331 none CC(C)(C)OC(=O)N1CCC[C@H]1[C@@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 32, 33, 33, 27, 14, 27, 14, 14, 14, 14, 6, 14, 6, 8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 101 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627094331 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094331 Building ZINC001627094334 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627094334 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/342 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627094334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094334 none CC(C)(C)OC(=O)N1CCC[C@H]1[C@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 32, 32, 19, 11, 19, 11, 11, 11, 11, 5, 11, 5, 8, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/343 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627094334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094334 none CC(C)(C)OC(=O)N1CCC[C@H]1[C@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 29, 31, 31, 16, 9, 16, 9, 9, 9, 9, 5, 9, 5, 7, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 90 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627094334 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 Building ZINC001627094334 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627094334 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 342) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@H]1[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627094334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094334 none CC(C)(C)OC(=O)N1CCC[C@H]1[C@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 32, 32, 19, 11, 19, 11, 11, 11, 11, 5, 11, 5, 8, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 343) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@H]1[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627094334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094334 none CC(C)(C)OC(=O)N1CCC[C@H]1[C@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 29, 31, 31, 16, 9, 16, 9, 9, 9, 9, 5, 9, 5, 7, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 90 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627094334 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094334 Building ZINC001627094336 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627094336 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/344 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627094336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094336 none CC(C)(C)OC(=O)N1CCC[C@@H]1[C@@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 31, 31, 17, 10, 17, 10, 10, 10, 10, 5, 10, 5, 8, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/345 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627094336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094336 none CC(C)(C)OC(=O)N1CCC[C@@H]1[C@@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 20, 12, 20, 12, 12, 12, 12, 5, 12, 5, 8, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 91 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627094336 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 Building ZINC001627094336 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627094336 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 344) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@@H]1[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627094336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094336 none CC(C)(C)OC(=O)N1CCC[C@@H]1[C@@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 31, 31, 17, 10, 17, 10, 10, 10, 10, 5, 10, 5, 8, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 345) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@@H]1[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627094336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094336 none CC(C)(C)OC(=O)N1CCC[C@@H]1[C@@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 20, 12, 20, 12, 12, 12, 12, 5, 12, 5, 8, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 91 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627094336 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094336 Building ZINC001627094338 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627094338 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/346 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627094338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094338 none CC(C)(C)OC(=O)N1CCC[C@@H]1[C@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 37, 37, 27, 12, 27, 12, 12, 12, 12, 5, 12, 5, 7, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/347 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627094338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094338 none CC(C)(C)OC(=O)N1CCC[C@@H]1[C@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 29, 29, 21, 12, 21, 12, 12, 12, 12, 5, 12, 5, 8, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 41 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]) total number of confs: 94 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627094338 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 Building ZINC001627094338 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627094338 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 346) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@@H]1[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627094338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094338 none CC(C)(C)OC(=O)N1CCC[C@@H]1[C@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 34, 37, 37, 27, 12, 27, 12, 12, 12, 12, 5, 12, 5, 7, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 115 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 347) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@@H]1[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627094338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627094338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001627094338 none CC(C)(C)OC(=O)N1CCC[C@@H]1[C@H]1CCCCN1C(=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.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', 'N.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'] 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, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 29, 29, 21, 12, 21, 12, 12, 12, 12, 5, 12, 5, 8, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 41 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]) total number of confs: 94 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627094338 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627094338 Building ZINC001627168352 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627168352 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/348 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627168352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627168352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001627168352 none O=C(Nc1ccnn1Cc1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 14, 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, 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, 4, 11, 11, 11, 11, 11, 28, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 11, 11, 28, 28, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/349 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627168352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627168352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001627168352 none O=C(Nc1ccnn1Cc1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 14, 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, 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, 4, 11, 11, 11, 11, 11, 28, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 11, 11, 28, 28, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627168352 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 Building ZINC001627168352 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627168352 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 348) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccnn1Cc1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627168352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627168352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001627168352 none O=C(Nc1ccnn1Cc1ccc(Cl)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 14, 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, 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, 4, 11, 11, 11, 11, 11, 28, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 11, 11, 28, 28, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 349) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccnn1Cc1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627168352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627168352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001627168352 none O=C(Nc1ccnn1Cc1ccc(Cl)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 16, 14, 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, 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, 4, 11, 11, 11, 11, 11, 28, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 6, 6, 4, 11, 11, 28, 28, 40, 40, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627168352 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627168352 Building ZINC001627300706 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627300706 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/350 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21) `ZINC001627300706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627300706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001627300706 none CCOC(=O)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 28, 28, 10, 28, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/351 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21) `ZINC001627300706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627300706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001627300706 none CCOC(=O)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 28, 3, 3, 3, 3, 3, 2, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 28, 28, 28, 28, 28, 10, 10, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627300706 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 Building ZINC001627300706 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627300706 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 350) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21) `ZINC001627300706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627300706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001627300706 none CCOC(=O)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 28, 28, 10, 28, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 351) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21) `ZINC001627300706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627300706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001627300706 none CCOC(=O)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 28, 3, 3, 3, 3, 3, 2, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 28, 28, 28, 28, 28, 10, 10, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627300706 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300706 Building ZINC001627300707 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627300707 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/352 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21) `ZINC001627300707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627300707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001627300707 none CCOC(=O)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 29, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 11, 11, 4, 4, 4, 4, 3, 3, 4, 4, 4, 4] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/353 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21) `ZINC001627300707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627300707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001627300707 none CCOC(=O)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 29, 29, 11, 29, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627300707 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 Building ZINC001627300707 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627300707 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 352) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21) `ZINC001627300707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627300707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001627300707 none CCOC(=O)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 29, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 11, 11, 4, 4, 4, 4, 3, 3, 4, 4, 4, 4] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 353) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21) `ZINC001627300707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627300707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001627300707 none CCOC(=O)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 29, 29, 11, 29, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627300707 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627300707 Building ZINC001627313501 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627313501 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/354 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C) `ZINC001627313501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627313501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001627313501 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 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, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 4, 4, 6, 6, 6, 12, 18, 18, 18, 18, 18, 18, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 8, 8, 18, 18, 18, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/355 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C) `ZINC001627313501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627313501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001627313501 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 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, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 4, 4, 7, 7, 7, 12, 13, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 8, 8, 13, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627313501 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 Building ZINC001627313501 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627313501 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 354) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C) `ZINC001627313501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627313501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001627313501 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 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, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 4, 4, 6, 6, 6, 12, 18, 18, 18, 18, 18, 18, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 8, 8, 18, 18, 18, 18, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 355) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C) `ZINC001627313501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627313501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001627313501 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@@H]1CCCN1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 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, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 4, 4, 7, 7, 7, 12, 13, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 8, 8, 13, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 17, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627313501 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313501 Building ZINC001627313502 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627313502 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/356 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C) `ZINC001627313502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627313502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001627313502 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 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, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 4, 4, 6, 6, 6, 11, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 7, 7, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/357 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C) `ZINC001627313502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627313502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001627313502 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 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, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 4, 4, 6, 6, 6, 12, 19, 19, 19, 19, 19, 19, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 8, 8, 19, 19, 19, 19, 19, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627313502 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 Building ZINC001627313502 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627313502 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 356) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C) `ZINC001627313502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627313502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001627313502 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 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, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 4, 4, 6, 6, 6, 11, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 7, 7, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 357) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C) `ZINC001627313502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627313502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001627313502 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)OC[C@H]1CCCN1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 11, 12, 5, 5, 7, 5, 5, 5, 8, 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, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 4, 4, 4, 6, 6, 6, 12, 19, 19, 19, 19, 19, 19, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 8, 8, 19, 19, 19, 19, 19, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627313502 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627313502 Building ZINC001627372604 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627372604 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/358 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)c1cccc(OC(F)(F)F)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627372604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627372604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627372604 none O=C(N[C@@H](CCO)c1cccc(OC(F)(F)F)c1)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 7, 5, 5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 3, 3, 7, 8, 3, 9, 9, 9, 9, 9, 40, 40, 40, 40, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 7, 7, 8, 8, 24, 9, 9, 9, 9, 3, 1, 3] 150 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: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/359 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)c1cccc(OC(F)(F)F)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627372604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627372604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627372604 none O=C(N[C@@H](CCO)c1cccc(OC(F)(F)F)c1)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 7, 5, 5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 4, 4, 8, 8, 4, 12, 12, 12, 12, 12, 49, 49, 49, 49, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 8, 24, 12, 12, 12, 12, 2, 1, 2] 150 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627372604 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 Building ZINC001627372604 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627372604 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 358) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)c1cccc(OC(F)(F)F)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627372604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627372604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627372604 none O=C(N[C@@H](CCO)c1cccc(OC(F)(F)F)c1)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 7, 5, 5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 3, 3, 7, 8, 3, 9, 9, 9, 9, 9, 40, 40, 40, 40, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 7, 7, 8, 8, 24, 9, 9, 9, 9, 3, 1, 3] 150 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: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 359) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)c1cccc(OC(F)(F)F)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627372604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627372604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627372604 none O=C(N[C@@H](CCO)c1cccc(OC(F)(F)F)c1)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 7, 5, 5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 4, 4, 8, 8, 4, 12, 12, 12, 12, 12, 49, 49, 49, 49, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 8, 24, 12, 12, 12, 12, 2, 1, 2] 150 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627372604 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372604 Building ZINC001627372606 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627372606 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/360 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CCO)c1cccc(OC(F)(F)F)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627372606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627372606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627372606 none O=C(N[C@H](CCO)c1cccc(OC(F)(F)F)c1)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 7, 5, 5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 4, 4, 8, 8, 4, 12, 12, 12, 12, 12, 50, 50, 50, 50, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 8, 24, 12, 12, 12, 12, 2, 1, 2] 150 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/361 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CCO)c1cccc(OC(F)(F)F)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627372606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627372606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627372606 none O=C(N[C@H](CCO)c1cccc(OC(F)(F)F)c1)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 7, 5, 5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 3, 3, 7, 7, 3, 11, 11, 11, 11, 11, 41, 41, 41, 41, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 7, 7, 7, 7, 21, 11, 11, 11, 11, 3, 1, 3] 150 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627372606 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 Building ZINC001627372606 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627372606 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 360) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@H](CCO)c1cccc(OC(F)(F)F)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627372606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627372606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627372606 none O=C(N[C@H](CCO)c1cccc(OC(F)(F)F)c1)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 7, 5, 5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 4, 4, 8, 8, 4, 12, 12, 12, 12, 12, 50, 50, 50, 50, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 8, 8, 8, 8, 24, 12, 12, 12, 12, 2, 1, 2] 150 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 361) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@H](CCO)c1cccc(OC(F)(F)F)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001627372606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627372606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627372606 none O=C(N[C@H](CCO)c1cccc(OC(F)(F)F)c1)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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, 7, 5, 5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 3, 3, 7, 7, 3, 11, 11, 11, 11, 11, 41, 41, 41, 41, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 7, 7, 7, 7, 21, 11, 11, 11, 11, 3, 1, 3] 150 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627372606 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627372606 Building ZINC001627378345 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627378345 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/362 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3ccc(Cl)cc3)c2)cc1Cl) `ZINC001627378345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627378345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627378345 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3ccc(Cl)cc3)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 10, 6, 6, 6, 10, 10, 10, 6, 6, 2, 10, 10, 19, 19, 19, 19, 19, 19, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/363 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3ccc(Cl)cc3)c2)cc1Cl) `ZINC001627378345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627378345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627378345 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3ccc(Cl)cc3)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 10, 6, 6, 6, 10, 10, 10, 6, 6, 2, 10, 10, 18, 18, 18, 18, 18, 18, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627378345 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 Building ZINC001627378345 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627378345 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 362) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3ccc(Cl)cc3)c2)cc1Cl) `ZINC001627378345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627378345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627378345 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3ccc(Cl)cc3)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 19, 10, 6, 6, 6, 10, 10, 10, 6, 6, 2, 10, 10, 19, 19, 19, 19, 19, 19, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 363) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3ccc(Cl)cc3)c2)cc1Cl) `ZINC001627378345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627378345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627378345 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3ccc(Cl)cc3)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 10, 6, 6, 6, 10, 10, 10, 6, 6, 2, 10, 10, 18, 18, 18, 18, 18, 18, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627378345 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627378345 Building ZINC001627386663 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627386663 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/364 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001627386663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627386663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001627386663 none CC(C)(C)OC(=O)NC(C)(C)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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 12, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 25, 34, 19, 8, 19, 19, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 8, 8, 39, 39, 39, 39, 39, 39, 39, 39, 39, 25, 19, 19, 19, 19, 19, 19, 8, 8, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 8, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/365 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001627386663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627386663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001627386663 none CC(C)(C)OC(=O)NC(C)(C)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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 12, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 27, 37, 20, 8, 20, 20, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 8, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 27, 20, 20, 20, 20, 20, 20, 8, 8, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 8, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627386663 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 Building ZINC001627386663 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627386663 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 364) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001627386663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627386663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001627386663 none CC(C)(C)OC(=O)NC(C)(C)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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 12, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 25, 34, 19, 8, 19, 19, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 8, 8, 39, 39, 39, 39, 39, 39, 39, 39, 39, 25, 19, 19, 19, 19, 19, 19, 8, 8, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 8, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 365) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC001627386663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627386663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001627386663 none CC(C)(C)OC(=O)NC(C)(C)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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 12, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 27, 37, 20, 8, 20, 20, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 8, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 27, 20, 20, 20, 20, 20, 20, 8, 8, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 8, 8] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627386663 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627386663 Building ZINC001627419978 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627419978 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/366 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/366' -> `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](c1ccncc1)C1CC1) `ZINC001627419978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627419978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627419978 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccncc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'N.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'] dock atom 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, 1, 1, 1, 8, 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] dock 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: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 10, 10, 8, 10, 10, 7, 9, 9, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 4, 10, 10, 10, 10, 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]) total number of confs: 83 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/367 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/367' -> `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](c1ccncc1)C1CC1) `ZINC001627419978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627419978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627419978 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccncc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'N.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'] dock atom 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, 1, 1, 1, 8, 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] dock 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, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 10, 8, 10, 10, 6, 8, 8, 4, 4, 4, 19, 19, 4, 19, 4, 4, 4, 3, 10, 10, 10, 10, 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]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627419978 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 Building ZINC001627419978 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627419978 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 366) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccncc1)C1CC1) `ZINC001627419978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627419978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627419978 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccncc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'N.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'] dock atom 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, 1, 1, 1, 8, 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] dock 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: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 4, 4, 4, 7, 7, 10, 10, 8, 10, 10, 7, 9, 9, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 4, 10, 10, 10, 10, 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]) total number of confs: 83 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 367) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccncc1)C1CC1) `ZINC001627419978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627419978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627419978 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccncc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'N.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'] dock atom 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, 1, 1, 1, 8, 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] dock 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, 19, 19, 4, 19, 19, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 10, 10, 8, 10, 10, 6, 8, 8, 4, 4, 4, 19, 19, 4, 19, 4, 4, 4, 3, 10, 10, 10, 10, 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]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627419978 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419978 Building ZINC001627419979 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627419979 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/368 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/368' -> `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](c1ccncc1)C1CC1) `ZINC001627419979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627419979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627419979 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccncc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'N.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'] dock atom 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, 1, 1, 1, 8, 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] dock 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: [3, 3, 3, 3, 3, 17, 17, 9, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 9, 9, 7, 9, 9, 6, 7, 7, 3, 3, 3, 17, 17, 12, 17, 3, 3, 3, 3, 9, 9, 9, 9, 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: 85 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/369 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/369' -> `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](c1ccncc1)C1CC1) `ZINC001627419979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627419979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627419979 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccncc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'N.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'] dock atom 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, 1, 1, 1, 8, 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] dock 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: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 13, 13, 13, 13, 13, 7, 10, 10, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 4, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627419979 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 Building ZINC001627419979 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627419979 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 368) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccncc1)C1CC1) `ZINC001627419979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627419979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627419979 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccncc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'N.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'] dock atom 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, 1, 1, 1, 8, 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] dock 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: [3, 3, 3, 3, 3, 17, 17, 9, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 9, 9, 7, 9, 9, 6, 7, 7, 3, 3, 3, 17, 17, 12, 17, 3, 3, 3, 3, 9, 9, 9, 9, 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: 85 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 369) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccncc1)C1CC1) `ZINC001627419979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627419979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001627419979 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccncc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'N.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'] dock atom 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, 1, 1, 1, 8, 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] dock 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: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 4, 4, 4, 7, 7, 13, 13, 13, 13, 13, 7, 10, 10, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 4, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627419979 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627419979 Building ZINC001627437277 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627437277 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/370 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(NC(=O)OC(C)(C)C)c1) `ZINC001627437277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627437277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001627437277 none Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(NC(=O)OC(C)(C)C)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 26, 39, 39, 39, 39, 39, 39, 17, 17, 17, 17, 17, 10, 10, 3, 3, 3, 3, 3, 17, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/371 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(NC(=O)OC(C)(C)C)c1) `ZINC001627437277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627437277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001627437277 none Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(NC(=O)OC(C)(C)C)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 26, 39, 39, 39, 39, 39, 39, 16, 16, 16, 16, 16, 8, 8, 2, 3, 3, 3, 3, 16, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627437277 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 Building ZINC001627437277 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627437277 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 370) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(NC(=O)OC(C)(C)C)c1) `ZINC001627437277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627437277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001627437277 none Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(NC(=O)OC(C)(C)C)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 26, 39, 39, 39, 39, 39, 39, 17, 17, 17, 17, 17, 10, 10, 3, 3, 3, 3, 3, 17, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 371) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(NC(=O)OC(C)(C)C)c1) `ZINC001627437277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627437277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001627437277 none Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc(NC(=O)OC(C)(C)C)c1 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 26, 39, 39, 39, 39, 39, 39, 16, 16, 16, 16, 16, 8, 8, 2, 3, 3, 3, 3, 16, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627437277 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627437277 Building ZINC001627445941 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627445941 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/372 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(cccc2OCC(F)(F)F)s1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001627445941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627445941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627445941 none O=C(Nc1nc2c(cccc2OCC(F)(F)F)s1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 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, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 19, 26, 26, 26, 26, 6, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 4, 6, 6, 6, 26, 26, 7, 8, 8, 7, 8, 8, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/373 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(cccc2OCC(F)(F)F)s1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001627445941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627445941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627445941 none O=C(Nc1nc2c(cccc2OCC(F)(F)F)s1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 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, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 19, 27, 27, 27, 27, 5, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 3, 5, 5, 5, 27, 27, 8, 9, 9, 8, 9, 9, 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, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627445941 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 Building ZINC001627445941 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627445941 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 372) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1nc2c(cccc2OCC(F)(F)F)s1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001627445941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627445941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627445941 none O=C(Nc1nc2c(cccc2OCC(F)(F)F)s1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 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, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 19, 26, 26, 26, 26, 6, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 4, 6, 6, 6, 26, 26, 7, 8, 8, 7, 8, 8, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 373) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1nc2c(cccc2OCC(F)(F)F)s1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001627445941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627445941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627445941 none O=C(Nc1nc2c(cccc2OCC(F)(F)F)s1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 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, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 19, 27, 27, 27, 27, 5, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 3, 5, 5, 5, 27, 27, 8, 9, 9, 8, 9, 9, 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, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627445941 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627445941 Building ZINC001627446169 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627446169 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/374 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cccc3OCC(F)(F)F)s2)cn1) `ZINC001627446169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627446169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001627446169 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cccc3OCC(F)(F)F)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 14, 1, 8, 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, 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] 0 hydrogens 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, 15, 15, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 19, 24, 24, 24, 24, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 4, 6, 6, 6, 24, 24, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/375 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cccc3OCC(F)(F)F)s2)cn1) `ZINC001627446169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627446169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001627446169 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cccc3OCC(F)(F)F)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 14, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 19, 25, 25, 25, 25, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 4, 6, 6, 6, 25, 25, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627446169 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 Building ZINC001627446169 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627446169 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 374) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cccc3OCC(F)(F)F)s2)cn1) `ZINC001627446169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627446169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001627446169 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(cccc3OCC(F)(F)F)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 14, 1, 8, 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, 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] 0 hydrogens 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, 15, 15, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 19, 24, 24, 24, 24, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 4, 6, 6, 6, 24, 24, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 375) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cccc3OCC(F)(F)F)s2)cn1) `ZINC001627446169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627446169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001627446169 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc3c(cccc3OCC(F)(F)F)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 14, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 19, 25, 25, 25, 25, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 4, 6, 6, 6, 25, 25, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627446169 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627446169 Building ZINC001627476545 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627476545 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/376 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1) `ZINC001627476545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627476545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001627476545 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1 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', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 3, 3, 6, 6, 6, 17, 17, 8, 17, 17, 17, 17, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 17, 17, 17, 7, 7, 3, 7, 7] 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]) total number of confs: 93 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/377 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1) `ZINC001627476545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627476545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001627476545 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1 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', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 4, 4, 11, 11, 11, 18, 18, 11, 18, 18, 18, 18, 4, 8, 8, 4, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 18, 18, 18, 8, 8, 4, 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]) total number of confs: 106 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627476545 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 Building ZINC001627476545 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627476545 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 376) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1) `ZINC001627476545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627476545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001627476545 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1 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', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 3, 3, 6, 6, 6, 17, 17, 8, 17, 17, 17, 17, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 17, 17, 17, 7, 7, 3, 7, 7] 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]) total number of confs: 93 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 377) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1) `ZINC001627476545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627476545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001627476545 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1 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', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 4, 4, 11, 11, 11, 18, 18, 11, 18, 18, 18, 18, 4, 8, 8, 4, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 18, 18, 18, 8, 8, 4, 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]) total number of confs: 106 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627476545 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476545 Building ZINC001627476546 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627476546 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/378 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1) `ZINC001627476546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627476546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001627476546 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1 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', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 4, 4, 11, 11, 11, 17, 17, 16, 17, 17, 17, 17, 4, 8, 8, 4, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 17, 17, 17, 8, 8, 4, 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]) total number of confs: 80 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/379 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1) `ZINC001627476546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627476546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001627476546 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1 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', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 3, 3, 6, 6, 6, 17, 17, 14, 17, 17, 17, 17, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 17, 17, 17, 7, 7, 3, 7, 7] 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]) total number of confs: 75 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627476546 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 Building ZINC001627476546 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627476546 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 378) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1) `ZINC001627476546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627476546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001627476546 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1 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', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 4, 4, 11, 11, 11, 17, 17, 16, 17, 17, 17, 17, 4, 8, 8, 4, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 11, 17, 17, 17, 8, 8, 4, 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]) total number of confs: 80 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 379) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1) `ZINC001627476546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627476546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001627476546 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](C(=O)Nc1ccc(Br)cc1F)c1ccccc1 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', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 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, 3, 3, 6, 6, 6, 17, 17, 14, 17, 17, 17, 17, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 6, 17, 17, 17, 7, 7, 3, 7, 7] 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]) total number of confs: 75 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627476546 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627476546 Building ZINC001627522516 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627522516 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/380 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)c2ccccc2)CC1) `ZINC001627522516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627522516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627522516 none CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)c2ccccc2)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 18, 18, 19, 19, 19, 19, 19, 10, 10, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 10, 10, 10, 10] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/381 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)c2ccccc2)CC1) `ZINC001627522516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627522516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627522516 none CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)c2ccccc2)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 18, 18, 21, 21, 20, 21, 21, 9, 9, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 9, 9, 9, 9] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627522516 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 Building ZINC001627522516 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627522516 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 380) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)c2ccccc2)CC1) `ZINC001627522516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627522516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627522516 none CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)c2ccccc2)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 18, 18, 19, 19, 19, 19, 19, 10, 10, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 10, 10, 10, 10] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 381) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)c2ccccc2)CC1) `ZINC001627522516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627522516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627522516 none CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)c2ccccc2)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 18, 18, 21, 21, 20, 21, 21, 9, 9, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 9, 9, 9, 9] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627522516 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627522516 Building ZINC001627547489 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627547489 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/382 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3cccc(Cl)c3)c2)cc1Cl) `ZINC001627547489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627547489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627547489 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3cccc(Cl)c3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.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, 11, 8, 5, 1, 1, 1, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 14, 25, 25, 25, 25, 25, 25, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 14, 14, 25, 25, 25, 25, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/369383/xbb-8058088.28/working/building/ZINC001627547489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/383 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3cccc(Cl)c3)c2)cc1Cl) `ZINC001627547489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627547489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627547489 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3cccc(Cl)c3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.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, 11, 8, 5, 1, 1, 1, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 13, 24, 24, 24, 24, 24, 24, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 13, 13, 24, 24, 24, 24, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/369383/xbb-8058088.28/working/building/ZINC001627547489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627547489 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489 Building ZINC001627547489 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627547489 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 382) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3cccc(Cl)c3)c2)cc1Cl) `ZINC001627547489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627547489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627547489 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3cccc(Cl)c3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.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, 11, 8, 5, 1, 1, 1, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 14, 25, 25, 25, 25, 25, 25, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 14, 14, 25, 25, 25, 25, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/369383/xbb-8058088.28/working/building/ZINC001627547489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 383) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3cccc(Cl)c3)c2)cc1Cl) `ZINC001627547489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627547489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001627547489 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(=O)n(Cc3cccc(Cl)c3)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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.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, 11, 8, 5, 1, 1, 1, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 13, 24, 24, 24, 24, 24, 24, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 13, 13, 24, 24, 24, 24, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/369383/xbb-8058088.28/working/building/ZINC001627547489 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627547489 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627547489 Building ZINC001627618218 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001627618218 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/384 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/385 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/386 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/386' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/387 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/387' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627618218 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 Building ZINC001627618218 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001627618218 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 384) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 385) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 386) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 387) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627618218 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 Building ZINC001627618218 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001627618218 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 384) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 385) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 386) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 387) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627618218 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 Building ZINC001627618218 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001627618218 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 384) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 385) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 386) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 387) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001627618218.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001627618218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001627618218 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 4, 4, 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, 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/369383/xbb-8058088.28/working/building/ZINC001627618218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627618218 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627618218 Building ZINC001627681863 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627681863 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/388 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@H]2C(C)C)CC1) `ZINC001627681863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627681863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627681863 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@H]2C(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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 10, 16, 16, 16, 16, 16, 16, 33, 33, 50, 50, 50, 50, 16, 16, 16, 20, 20, 16, 16, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/389 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@H]2C(C)C)CC1) `ZINC001627681863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627681863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627681863 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@H]2C(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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 9, 17, 17, 17, 17, 17, 17, 33, 33, 50, 50, 50, 50, 17, 17, 17, 21, 21, 17, 17, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 21, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627681863 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 Building ZINC001627681863 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627681863 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 388) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@H]2C(C)C)CC1) `ZINC001627681863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627681863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627681863 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@H]2C(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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 10, 16, 16, 16, 16, 16, 16, 33, 33, 50, 50, 50, 50, 16, 16, 16, 20, 20, 16, 16, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 389) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@H]2C(C)C)CC1) `ZINC001627681863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627681863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627681863 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@H]2C(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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 9, 17, 17, 17, 17, 17, 17, 33, 33, 50, 50, 50, 50, 17, 17, 17, 21, 21, 17, 17, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 21, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627681863 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681863 Building ZINC001627681864 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627681864 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/390 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@@H]2C(C)C)CC1) `ZINC001627681864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627681864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627681864 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@@H]2C(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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 9, 18, 18, 18, 18, 18, 18, 35, 35, 50, 50, 50, 50, 18, 18, 18, 22, 22, 18, 18, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/391 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@@H]2C(C)C)CC1) `ZINC001627681864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627681864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627681864 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@@H]2C(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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 11, 20, 20, 20, 20, 20, 20, 35, 35, 50, 50, 50, 50, 20, 20, 20, 24, 24, 20, 20, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627681864 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 Building ZINC001627681864 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627681864 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 390) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@@H]2C(C)C)CC1) `ZINC001627681864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627681864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627681864 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@@H]2C(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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 9, 18, 18, 18, 18, 18, 18, 35, 35, 50, 50, 50, 50, 18, 18, 18, 22, 22, 18, 18, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 391) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@@H]2C(C)C)CC1) `ZINC001627681864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627681864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627681864 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CN(C(=O)OC(C)(C)C)[C@@H]2C(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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 11, 20, 20, 20, 20, 20, 20, 35, 35, 50, 50, 50, 50, 20, 20, 20, 24, 24, 20, 20, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627681864 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627681864 Building ZINC001627721384 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627721384 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/392 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21) `ZINC001627721384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627721384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001627721384 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 30, 39, 13, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 39, 39, 39, 13, 13, 3, 3, 1, 3, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/393 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21) `ZINC001627721384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627721384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001627721384 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 29, 38, 13, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 38, 38, 38, 13, 13, 3, 3, 1, 3, 34, 34, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627721384 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 Building ZINC001627721384 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627721384 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 392) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21) `ZINC001627721384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627721384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001627721384 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 30, 39, 13, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 39, 39, 39, 13, 13, 3, 3, 1, 3, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 393) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21) `ZINC001627721384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627721384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001627721384 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 29, 38, 13, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 38, 38, 38, 13, 13, 3, 3, 1, 3, 34, 34, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627721384 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721384 Building ZINC001627721385 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627721385 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/394 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21) `ZINC001627721385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627721385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001627721385 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 29, 38, 13, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 38, 38, 38, 13, 13, 3, 3, 1, 3, 34, 34, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/395 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21) `ZINC001627721385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627721385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001627721385 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 30, 39, 13, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 39, 39, 39, 13, 13, 3, 3, 1, 3, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627721385 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 Building ZINC001627721385 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627721385 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 394) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21) `ZINC001627721385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627721385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001627721385 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 29, 38, 13, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 27, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 38, 38, 38, 13, 13, 3, 3, 1, 3, 34, 34, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 395) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21) `ZINC001627721385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627721385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001627721385 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1cccc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 30, 39, 13, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 28, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 39, 39, 39, 13, 13, 3, 3, 1, 3, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627721385 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627721385 Building ZINC001627724909 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627724909 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/396 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001627724909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627724909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627724909 none CC(C)(C)OC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [43, 43, 43, 43, 27, 15, 27, 15, 15, 15, 15, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 43, 43, 43, 43, 43, 43, 43, 43, 43, 15, 15, 15, 15, 15, 15, 15, 15, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/397 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001627724909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627724909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627724909 none CC(C)(C)OC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [43, 43, 43, 43, 25, 12, 25, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 43, 43, 43, 43, 43, 43, 43, 43, 43, 12, 12, 12, 12, 12, 12, 12, 12, 4, 3, 1, 3, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627724909 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 Building ZINC001627724909 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627724909 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 396) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001627724909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627724909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627724909 none CC(C)(C)OC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [43, 43, 43, 43, 27, 15, 27, 15, 15, 15, 15, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 43, 43, 43, 43, 43, 43, 43, 43, 43, 15, 15, 15, 15, 15, 15, 15, 15, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 397) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001627724909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627724909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627724909 none CC(C)(C)OC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [43, 43, 43, 43, 25, 12, 25, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 43, 43, 43, 43, 43, 43, 43, 43, 43, 12, 12, 12, 12, 12, 12, 12, 12, 4, 3, 1, 3, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627724909 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627724909 Building ZINC001627775769 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627775769 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/398 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Br)cc1Oc1ccccc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001627775769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627775769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627775769 none O=C(NCc1ccc(Br)cc1Oc1ccccc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 12, 32, 32, 21, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 12, 12, 32, 32, 32, 50, 50, 50, 50, 50, 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: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/399 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Br)cc1Oc1ccccc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001627775769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627775769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627775769 none O=C(NCc1ccc(Br)cc1Oc1ccccc1)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 12, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 12, 12, 32, 32, 32, 50, 50, 50, 50, 50, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627775769 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 Building ZINC001627775769 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627775769 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 398) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NCc1ccc(Br)cc1Oc1ccccc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001627775769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627775769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627775769 none O=C(NCc1ccc(Br)cc1Oc1ccccc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 12, 32, 32, 21, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 12, 12, 32, 32, 32, 50, 50, 50, 50, 50, 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: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 399) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NCc1ccc(Br)cc1Oc1ccccc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001627775769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627775769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001627775769 none O=C(NCc1ccc(Br)cc1Oc1ccccc1)[C@]([O-])([SiH3])c1ccc(O)cc1 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 12, 32, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 12, 12, 32, 32, 32, 50, 50, 50, 50, 50, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627775769 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627775769 Building ZINC001627786978 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627786978 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/400 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F) `ZINC001627786978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627786978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001627786978 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 24, 25, 25, 36, 36, 36, 36, 36, 47, 47, 36, 47, 47, 36, 36, 25, 25, 25, 25, 6, 6, 6, 5, 5, 5, 5, 6, 24, 24, 36, 36, 36, 47, 47, 45, 47, 47, 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]) total number of confs: 196 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/401 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F) `ZINC001627786978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627786978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001627786978 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 22, 27, 27, 43, 43, 43, 43, 43, 46, 46, 43, 46, 46, 43, 43, 27, 27, 27, 27, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 43, 43, 43, 46, 46, 43, 46, 46, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 161 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627786978 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 Building ZINC001627786978 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627786978 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 400) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)NC[C@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F) `ZINC001627786978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627786978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001627786978 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 24, 25, 25, 36, 36, 36, 36, 36, 47, 47, 36, 47, 47, 36, 36, 25, 25, 25, 25, 6, 6, 6, 5, 5, 5, 5, 6, 24, 24, 36, 36, 36, 47, 47, 45, 47, 47, 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]) total number of confs: 196 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 401) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)NC[C@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F) `ZINC001627786978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627786978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001627786978 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 22, 27, 27, 43, 43, 43, 43, 43, 46, 46, 43, 46, 46, 43, 43, 27, 27, 27, 27, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 43, 43, 43, 46, 46, 43, 46, 46, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 161 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627786978 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786978 Building ZINC001627786979 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627786979 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/402 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F) `ZINC001627786979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627786979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001627786979 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 23, 28, 28, 42, 42, 42, 42, 42, 46, 46, 46, 46, 46, 42, 42, 28, 28, 28, 28, 3, 3, 3, 3, 3, 3, 3, 6, 23, 23, 42, 42, 42, 46, 46, 46, 46, 46, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 153 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/403 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F) `ZINC001627786979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627786979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001627786979 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 24, 25, 25, 37, 37, 37, 37, 37, 48, 48, 48, 48, 48, 37, 37, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 6, 24, 24, 37, 37, 37, 48, 48, 48, 48, 48, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627786979 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 Building ZINC001627786979 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627786979 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 402) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F) `ZINC001627786979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627786979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001627786979 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 23, 28, 28, 42, 42, 42, 42, 42, 46, 46, 46, 46, 46, 42, 42, 28, 28, 28, 28, 3, 3, 3, 3, 3, 3, 3, 6, 23, 23, 42, 42, 42, 46, 46, 46, 46, 46, 42, 42, 42] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 153 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 403) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F) `ZINC001627786979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627786979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001627786979 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c(C)nn(c2ccccc2)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 6, 6, 6, 24, 25, 25, 37, 37, 37, 37, 37, 48, 48, 48, 48, 48, 37, 37, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 6, 24, 24, 37, 37, 37, 48, 48, 48, 48, 48, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627786979 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627786979 Building ZINC001627855661 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627855661 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/404 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1) `ZINC001627855661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627855661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001627855661 none CCN(CC)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 23, 29, 6, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 2, 3, 3, 2, 3, 3, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 9, 9, 6, 6, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 3, 2, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 159 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/405 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1) `ZINC001627855661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627855661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001627855661 none CCN(CC)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 11, 26, 29, 10, 3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 3, 6, 6, 3, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 10, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 3, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 143 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627855661 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 Building ZINC001627855661 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627855661 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 404) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1) `ZINC001627855661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627855661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001627855661 none CCN(CC)CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 23, 29, 6, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 2, 3, 3, 2, 3, 3, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 9, 9, 6, 6, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 3, 2, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 159 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 405) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1) `ZINC001627855661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627855661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001627855661 none CCN(CC)CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 11, 26, 29, 10, 3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 3, 6, 6, 3, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 10, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 3, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 143 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627855661 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855661 Building ZINC001627855672 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627855672 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/406 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1) `ZINC001627855672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627855672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001627855672 none CCN(CC)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 10, 27, 30, 9, 3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 6, 6, 3, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 9, 9, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 154 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/407 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1) `ZINC001627855672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627855672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001627855672 none CCN(CC)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 23, 9, 23, 28, 6, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 2, 3, 3, 29, 29, 29, 29, 29, 28, 28, 28, 28, 28, 9, 9, 6, 6, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 2, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 153 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627855672 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 Building ZINC001627855672 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627855672 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 406) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCN(CC)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1) `ZINC001627855672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627855672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001627855672 none CCN(CC)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 10, 27, 30, 9, 3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 3, 6, 6, 3, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 9, 9, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 154 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 407) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCN(CC)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1) `ZINC001627855672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627855672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001627855672 none CCN(CC)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 23, 9, 23, 28, 6, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 2, 3, 3, 29, 29, 29, 29, 29, 28, 28, 28, 28, 28, 9, 9, 6, 6, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 2, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 153 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627855672 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627855672 Building ZINC001627925630 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627925630 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/408 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627925630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627925630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001627925630 none O=C(N[C@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 14, 14, 10, 14, 14, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 4, 14, 14, 10, 14, 14, 30, 30, 30, 30, 6, 6] 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]) total number of confs: 87 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/409 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627925630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627925630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001627925630 none O=C(N[C@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 13, 13, 8, 13, 13, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 7, 7, 7, 7, 7, 4, 13, 13, 8, 13, 13, 28, 28, 28, 28, 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]) total number of confs: 85 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627925630 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 Building ZINC001627925630 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627925630 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 408) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627925630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627925630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001627925630 none O=C(N[C@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 14, 14, 10, 14, 14, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 4, 14, 14, 10, 14, 14, 30, 30, 30, 30, 6, 6] 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]) total number of confs: 87 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 409) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627925630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627925630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001627925630 none O=C(N[C@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 13, 13, 8, 13, 13, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 7, 7, 7, 7, 7, 4, 13, 13, 8, 13, 13, 28, 28, 28, 28, 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]) total number of confs: 85 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627925630 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925630 Building ZINC001627925631 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627925631 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/410 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627925631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627925631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001627925631 none O=C(N[C@@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 13, 13, 9, 13, 13, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 7, 7, 7, 7, 7, 4, 13, 13, 9, 13, 13, 28, 28, 28, 28, 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]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/411 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627925631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627925631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001627925631 none O=C(N[C@@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 14, 14, 8, 14, 14, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 7, 7, 7, 7, 7, 4, 14, 14, 8, 14, 14, 29, 29, 29, 29, 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]) total number of confs: 92 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627925631 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 Building ZINC001627925631 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627925631 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 410) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627925631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627925631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001627925631 none O=C(N[C@@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 13, 13, 9, 13, 13, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 7, 7, 7, 7, 7, 4, 13, 13, 9, 13, 13, 28, 28, 28, 28, 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]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 411) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001627925631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627925631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001627925631 none O=C(N[C@@H](c1ccccc1)c1ccc2nc[nH]c2c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 14, 14, 8, 14, 14, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 7, 7, 7, 7, 7, 4, 14, 14, 8, 14, 14, 29, 29, 29, 29, 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]) total number of confs: 92 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627925631 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627925631 Building ZINC001627932718 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627932718 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/412 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@H]2CNC(=O)OC(C)(C)C)CC1) `ZINC001627932718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627932718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627932718 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@H]2CNC(=O)OC(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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 36, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 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, 62, 63]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/413 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@H]2CNC(=O)OC(C)(C)C)CC1) `ZINC001627932718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627932718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627932718 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@H]2CNC(=O)OC(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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 36, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627932718 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 Building ZINC001627932718 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627932718 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 412) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@H]2CNC(=O)OC(C)(C)C)CC1) `ZINC001627932718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627932718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627932718 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@H]2CNC(=O)OC(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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 36, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 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, 62, 63]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 413) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@H]2CNC(=O)OC(C)(C)C)CC1) `ZINC001627932718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627932718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627932718 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@H]2CNC(=O)OC(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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 36, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627932718 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932718 Building ZINC001627932719 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627932719 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/414 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@@H]2CNC(=O)OC(C)(C)C)CC1) `ZINC001627932719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627932719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627932719 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@@H]2CNC(=O)OC(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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 21, 41, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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/369383/xbb-8058088.28/working/building/ZINC001627932719 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/415 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@@H]2CNC(=O)OC(C)(C)C)CC1) `ZINC001627932719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627932719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627932719 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@@H]2CNC(=O)OC(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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 36, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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/369383/xbb-8058088.28/working/building/ZINC001627932719 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627932719 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719 Building ZINC001627932719 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627932719 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 414) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@@H]2CNC(=O)OC(C)(C)C)CC1) `ZINC001627932719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627932719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627932719 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@@H]2CNC(=O)OC(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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 21, 41, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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/369383/xbb-8058088.28/working/building/ZINC001627932719 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 415) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@@H]2CNC(=O)OC(C)(C)C)CC1) `ZINC001627932719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627932719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001627932719 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC2(CCC[C@@H]2CNC(=O)OC(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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 36, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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/369383/xbb-8058088.28/working/building/ZINC001627932719 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627932719 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627932719 Building ZINC001627998756 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627998756 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/416 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627998756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627998756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001627998756 none O=C(Nc1ccnn1Cc1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 29, 30, 30, 29, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 14, 14, 29, 29, 30, 30, 30, 30, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/417 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627998756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627998756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001627998756 none O=C(Nc1ccnn1Cc1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 15, 30, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 15, 15, 30, 30, 31, 31, 31, 31, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627998756 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 Building ZINC001627998756 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001627998756 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 416) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627998756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001627998756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001627998756 none O=C(Nc1ccnn1Cc1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 29, 30, 30, 29, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 14, 14, 29, 29, 30, 30, 30, 30, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 417) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001627998756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001627998756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001627998756 none O=C(Nc1ccnn1Cc1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 15, 30, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 15, 15, 30, 30, 31, 31, 31, 31, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001627998756 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001627998756 Building ZINC001628010138 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628010138 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/418 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1)C(=O)OC(C)(C)C) `ZINC001628010138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628010138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001628010138 none CN(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 32, 49, 49, 49, 49, 49, 49, 32, 32, 32, 14, 14, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 8, 8, 49, 49, 49, 49, 49, 49, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/419 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1)C(=O)OC(C)(C)C) `ZINC001628010138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628010138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001628010138 none CN(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 32, 49, 49, 49, 49, 49, 49, 32, 32, 32, 13, 13, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 8, 8, 49, 49, 49, 49, 49, 49, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628010138 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 Building ZINC001628010138 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628010138 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 418) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1)C(=O)OC(C)(C)C) `ZINC001628010138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628010138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001628010138 none CN(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 32, 49, 49, 49, 49, 49, 49, 32, 32, 32, 14, 14, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 8, 8, 49, 49, 49, 49, 49, 49, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 419) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1)C(=O)OC(C)(C)C) `ZINC001628010138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628010138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001628010138 none CN(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cc1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 32, 49, 49, 49, 49, 49, 49, 32, 32, 32, 13, 13, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 8, 8, 49, 49, 49, 49, 49, 49, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628010138 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628010138 Building ZINC001628076204 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628076204 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/420 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1CCCN(C(=O)OC(C)(C)C)C1) `ZINC001628076204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628076204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628076204 none CCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 23, 23, 23, 23, 23, 23, 34, 34, 47, 48, 48, 48, 23, 8, 8, 8, 8, 8, 2, 1, 2, 23, 23, 23, 23, 23, 23, 48, 48, 48, 48, 48, 48, 48, 48, 48, 23, 23] 50 rigid atoms, others: [5, 6, 7, 3] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/421 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1CCCN(C(=O)OC(C)(C)C)C1) `ZINC001628076204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628076204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628076204 none CCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 20, 20, 20, 20, 20, 20, 33, 33, 47, 48, 48, 48, 20, 6, 6, 6, 6, 6, 3, 1, 3, 20, 20, 20, 20, 20, 20, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20] 50 rigid atoms, others: [5, 6, 7, 3] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628076204 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 Building ZINC001628076204 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628076204 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 420) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1CCCN(C(=O)OC(C)(C)C)C1) `ZINC001628076204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628076204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628076204 none CCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 23, 23, 23, 23, 23, 23, 34, 34, 47, 48, 48, 48, 23, 8, 8, 8, 8, 8, 2, 1, 2, 23, 23, 23, 23, 23, 23, 48, 48, 48, 48, 48, 48, 48, 48, 48, 23, 23] 50 rigid atoms, others: [5, 6, 7, 3] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 141 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 421) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1CCCN(C(=O)OC(C)(C)C)C1) `ZINC001628076204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628076204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628076204 none CCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H]1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 20, 20, 20, 20, 20, 20, 33, 33, 47, 48, 48, 48, 20, 6, 6, 6, 6, 6, 3, 1, 3, 20, 20, 20, 20, 20, 20, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 20] 50 rigid atoms, others: [5, 6, 7, 3] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628076204 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076204 Building ZINC001628076206 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628076206 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/422 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1CCCN(C(=O)OC(C)(C)C)C1) `ZINC001628076206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628076206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628076206 none CCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 17, 17, 17, 17, 17, 17, 29, 29, 47, 47, 47, 47, 17, 6, 6, 6, 6, 6, 2, 1, 2, 17, 17, 17, 17, 17, 17, 47, 47, 47, 47, 47, 47, 47, 47, 47, 17, 17] 50 rigid atoms, others: [5, 6, 7, 3] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/423 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1CCCN(C(=O)OC(C)(C)C)C1) `ZINC001628076206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628076206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628076206 none CCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 15, 15, 15, 15, 15, 15, 25, 25, 41, 41, 41, 41, 15, 7, 7, 7, 7, 7, 3, 1, 3, 15, 15, 15, 15, 15, 15, 41, 41, 41, 41, 41, 41, 41, 41, 41, 15, 15] 50 rigid atoms, others: [5, 6, 7, 3] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 119 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628076206 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 Building ZINC001628076206 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628076206 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 422) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1CCCN(C(=O)OC(C)(C)C)C1) `ZINC001628076206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628076206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628076206 none CCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 17, 17, 17, 17, 17, 17, 29, 29, 47, 47, 47, 47, 17, 6, 6, 6, 6, 6, 2, 1, 2, 17, 17, 17, 17, 17, 17, 47, 47, 47, 47, 47, 47, 47, 47, 47, 17, 17] 50 rigid atoms, others: [5, 6, 7, 3] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 423) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1CCCN(C(=O)OC(C)(C)C)C1) `ZINC001628076206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628076206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001628076206 none CCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H]1CCCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 15, 15, 15, 15, 15, 15, 25, 25, 41, 41, 41, 41, 15, 7, 7, 7, 7, 7, 3, 1, 3, 15, 15, 15, 15, 15, 15, 41, 41, 41, 41, 41, 41, 41, 41, 41, 15, 15] 50 rigid atoms, others: [5, 6, 7, 3] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 119 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628076206 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628076206 Building ZINC001628091628 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628091628 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/424 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/424' -> `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])c2cnn(c3ccccc3)c2)c1O) `ZINC001628091628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628091628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001628091628 none CC(C)(C)c1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)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.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 5, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 16, 16, 11, 16, 16, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 11, 16, 16, 11, 16, 16, 11, 36] 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, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/425 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/425' -> `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])c2cnn(c3ccccc3)c2)c1O) `ZINC001628091628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628091628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001628091628 none CC(C)(C)c1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)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.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 4, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 10, 16, 16, 10, 16, 16, 10, 38] 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, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628091628 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 Building ZINC001628091628 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628091628 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 424) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)c1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1O) `ZINC001628091628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628091628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001628091628 none CC(C)(C)c1cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)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.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 5, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 16, 16, 11, 16, 16, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 11, 16, 16, 11, 16, 16, 11, 36] 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, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 425) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)c1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1O) `ZINC001628091628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628091628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001628091628 none CC(C)(C)c1cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)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.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 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, 6] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 4, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 10, 16, 16, 10, 16, 16, 10, 38] 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, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628091628 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628091628 Building ZINC001628423710 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628423710 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/426 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3Cl)c2)c1) `ZINC001628423710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628423710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001628423710 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 2, 11, 11, 15, 15, 15, 21, 28, 28, 23, 28, 28, 28, 11, 4, 4, 4, 4, 2, 4, 4, 2, 11, 11, 2, 21, 28, 28, 28, 28, 11, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/427 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3Cl)c2)c1) `ZINC001628423710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628423710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001628423710 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 11, 11, 11, 15, 15, 15, 21, 27, 27, 27, 27, 27, 27, 11, 4, 4, 4, 4, 2, 4, 4, 2, 11, 11, 11, 21, 27, 27, 27, 27, 11, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628423710 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 Building ZINC001628423710 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628423710 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 426) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3Cl)c2)c1) `ZINC001628423710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628423710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001628423710 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 2, 11, 11, 15, 15, 15, 21, 28, 28, 23, 28, 28, 28, 11, 4, 4, 4, 4, 2, 4, 4, 2, 11, 11, 2, 21, 28, 28, 28, 28, 11, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 427) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3Cl)c2)c1) `ZINC001628423710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628423710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001628423710 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2cccc(S(=O)(=O)Nc3ccccc3Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 11, 11, 11, 15, 15, 15, 21, 27, 27, 27, 27, 27, 27, 11, 4, 4, 4, 4, 2, 4, 4, 2, 11, 11, 11, 21, 27, 27, 27, 27, 11, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628423710 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628423710 Building ZINC001628427904 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628427904 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/428 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1) `ZINC001628427904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628427904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001628427904 none COc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 20, 20, 43, 43, 20, 20, 10, 20, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 43, 43, 43, 43, 43, 43, 43, 20, 10, 10, 3, 4, 4, 4, 4, 10, 10, 43, 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, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/429 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1) `ZINC001628427904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628427904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001628427904 none COc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 20, 20, 3, 20, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 37, 37, 37, 37, 37, 37, 37, 20, 11, 11, 3, 4, 4, 4, 4, 11, 11, 37, 37] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628427904 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 Building ZINC001628427904 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628427904 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 428) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1) `ZINC001628427904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628427904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001628427904 none COc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 20, 20, 43, 43, 20, 20, 10, 20, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 43, 43, 43, 43, 43, 43, 43, 20, 10, 10, 3, 4, 4, 4, 4, 10, 10, 43, 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, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 429) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1) `ZINC001628427904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628427904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001628427904 none COc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 20, 20, 3, 20, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 37, 37, 37, 37, 37, 37, 37, 20, 11, 11, 3, 4, 4, 4, 4, 11, 11, 37, 37] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628427904 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628427904 Building ZINC001628522086 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628522086 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/430 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/430' -> `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]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628522086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522086 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 19, 24, 19, 19, 19, 19, 5, 19, 5, 7, 5, 5, 5, 3, 2, 5, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 5, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 19, 19] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/431 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/431' -> `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]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628522086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522086 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 17, 24, 17, 17, 17, 17, 4, 17, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 4, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 17, 17] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628522086 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 Building ZINC001628522086 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628522086 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 430) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)OC(=O)N1CCC[C@@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628522086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522086 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 19, 24, 19, 19, 19, 19, 5, 19, 5, 7, 5, 5, 5, 3, 2, 5, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 5, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 19, 19] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 431) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)OC(=O)N1CCC[C@@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628522086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522086 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 17, 24, 17, 17, 17, 17, 4, 17, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 4, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 17, 17] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628522086 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522086 Building ZINC001628522087 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628522087 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/432 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/432' -> `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]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628522087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522087 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 18, 25, 18, 18, 18, 18, 5, 18, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 5, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 18, 18] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 95 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/433 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/433' -> `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]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628522087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522087 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 16, 24, 16, 16, 16, 16, 5, 16, 5, 5, 5, 5, 5, 3, 2, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 16, 16] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 81 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628522087 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 Building ZINC001628522087 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628522087 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 432) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628522087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522087 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 18, 25, 18, 18, 18, 18, 5, 18, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 5, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 18, 18] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 95 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 433) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628522087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522087 none CC(C)(C)OC(=O)N1CCC[C@@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 16, 24, 16, 16, 16, 16, 5, 16, 5, 5, 5, 5, 5, 3, 2, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 16, 16] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 81 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628522087 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522087 Building ZINC001628522088 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628522088 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/434 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/434' -> `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]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628522088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522088 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 27, 19, 27, 19, 19, 19, 19, 5, 19, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 5, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 19, 19] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 105 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/435 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/435' -> `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]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628522088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522088 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 22, 17, 17, 17, 17, 5, 17, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 5, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 17, 17] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 88 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628522088 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 Building ZINC001628522088 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628522088 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 434) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)OC(=O)N1CCC[C@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628522088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522088 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 27, 19, 27, 19, 19, 19, 19, 5, 19, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 5, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 19, 19] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 105 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 435) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)OC(=O)N1CCC[C@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628522088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522088 none CC(C)(C)OC(=O)N1CCC[C@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 22, 17, 17, 17, 17, 5, 17, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 5, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 17, 17] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 88 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628522088 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522088 Building ZINC001628522089 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628522089 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/436 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/436' -> `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]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628522089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522089 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 17, 25, 17, 17, 17, 17, 4, 17, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 4, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/437 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/437' -> `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]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628522089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522089 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 15, 22, 15, 15, 15, 15, 4, 15, 4, 5, 4, 4, 4, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 76 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628522089 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 Building ZINC001628522089 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628522089 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 436) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628522089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522089 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 17, 25, 17, 17, 17, 17, 4, 17, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 4, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 437) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001628522089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628522089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001628522089 none CC(C)(C)OC(=O)N1CCC[C@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 15, 22, 15, 15, 15, 15, 4, 15, 4, 5, 4, 4, 4, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 76 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628522089 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628522089 Building ZINC001628524631 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628524631 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/438 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001628524631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628524631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001628524631 none CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 4, 8, 16, 36, 36, 36, 50, 50, 47, 50, 50, 50, 50, 50, 50, 50, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 36, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/439 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001628524631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628524631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001628524631 none CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 4, 8, 16, 35, 35, 35, 50, 50, 35, 47, 50, 50, 50, 50, 50, 50, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 35, 50, 50, 50, 2, 2, 4, 2, 2] 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]) total number of confs: 257 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628524631 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 Building ZINC001628524631 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628524631 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 438) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001628524631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628524631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001628524631 none CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 4, 8, 16, 36, 36, 36, 50, 50, 47, 50, 50, 50, 50, 50, 50, 50, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 36, 50, 50, 50, 3, 3, 6, 3, 3] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 210 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 439) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001628524631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628524631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001628524631 none CC(C)N(CC(=O)Nc1ccc(Cl)cc1C(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 4, 8, 16, 35, 35, 35, 50, 50, 35, 47, 50, 50, 50, 50, 50, 50, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 35, 50, 50, 50, 2, 2, 4, 2, 2] 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]) total number of confs: 257 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628524631 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628524631 Building ZINC001628681386 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628681386 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/440 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/440' -> `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(C)cc2)CC1) `ZINC001628681386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628681386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001628681386 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(C)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', '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'] 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, 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] 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 42, 20, 42, 42, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 20, 20, 48, 48, 48, 48, 48, 50, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/441 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/441' -> `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(C)cc2)CC1) `ZINC001628681386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628681386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001628681386 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(C)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', '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'] 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, 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] 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, 7, 7, 7] 0 hydrogens 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, 43, 19, 43, 43, 50, 50, 43, 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, 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, 49, 50, 51]) total number of confs: 238 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628681386 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 Building ZINC001628681386 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628681386 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 440) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)CC1) `ZINC001628681386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628681386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001628681386 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(C)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', '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'] 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, 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] 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 42, 20, 42, 42, 50, 50, 50, 50, 50, 50, 20, 20, 20, 8, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 20, 20, 48, 48, 48, 48, 48, 50, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 441) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)CC1) `ZINC001628681386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628681386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001628681386 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(C)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', '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'] 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, 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] 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, 7, 7, 7] 0 hydrogens 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, 43, 19, 43, 43, 50, 50, 43, 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, 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, 49, 50, 51]) total number of confs: 238 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628681386 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681386 Building ZINC001628681387 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628681387 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/442 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/442' -> `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(C)cc2)CC1) `ZINC001628681387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628681387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001628681387 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(C)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', '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'] 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, 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] 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, 7, 7, 7] 0 hydrogens need 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, 8, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 20, 20, 50, 50, 50, 50, 50, 48, 48, 48, 48, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/443 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/443' -> `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(C)cc2)CC1) `ZINC001628681387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628681387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001628681387 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(C)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', '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'] 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, 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] 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, 7, 7, 7] 0 hydrogens need 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, 19, 43, 43, 49, 49, 49, 49, 49, 49, 19, 19, 19, 7, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 50, 50, 50, 50, 50, 49, 49, 49, 49, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 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, 51]) total number of confs: 206 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628681387 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 Building ZINC001628681387 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628681387 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 442) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)CC1) `ZINC001628681387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628681387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001628681387 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(C)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', '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'] 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, 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] 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, 7, 7, 7] 0 hydrogens need 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, 8, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 20, 20, 50, 50, 50, 50, 50, 48, 48, 48, 48, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 443) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)CC1) `ZINC001628681387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628681387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001628681387 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(C)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', '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'] 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, 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] 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, 7, 7, 7] 0 hydrogens need 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, 19, 43, 43, 49, 49, 49, 49, 49, 49, 19, 19, 19, 7, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 50, 50, 50, 50, 50, 49, 49, 49, 49, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 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, 51]) total number of confs: 206 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628681387 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628681387 Building ZINC001628723845 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628723845 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/444 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001628723845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628723845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001628723845 none C[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 31, 31, 47, 47, 46, 47, 47, 47, 47, 17, 17, 17, 7, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 17, 17, 31, 31, 31, 47, 47, 47, 17, 17, 17, 17, 3, 3, 3, 17, 17, 17, 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]) total number of confs: 124 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/445 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001628723845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628723845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001628723845 none C[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 15, 31, 31, 47, 47, 44, 47, 47, 47, 47, 15, 15, 15, 5, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 31, 31, 31, 47, 47, 47, 15, 15, 15, 15, 3, 1, 3, 15, 15, 15, 15] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628723845 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 Building ZINC001628723845 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628723845 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 444) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001628723845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628723845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001628723845 none C[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 31, 31, 47, 47, 46, 47, 47, 47, 47, 17, 17, 17, 7, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 17, 17, 31, 31, 31, 47, 47, 47, 17, 17, 17, 17, 3, 3, 3, 17, 17, 17, 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]) total number of confs: 124 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 445) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001628723845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628723845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001628723845 none C[C@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 15, 31, 31, 47, 47, 44, 47, 47, 47, 47, 15, 15, 15, 5, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 31, 31, 31, 47, 47, 47, 15, 15, 15, 15, 3, 1, 3, 15, 15, 15, 15] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628723845 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723845 Building ZINC001628723847 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628723847 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/446 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001628723847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628723847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001628723847 none C[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 30, 30, 45, 45, 30, 45, 45, 45, 45, 16, 16, 16, 6, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 16, 16, 30, 30, 30, 45, 45, 45, 16, 16, 16, 16, 3, 3, 3, 16, 16, 16, 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]) total number of confs: 186 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/447 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001628723847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628723847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001628723847 none C[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 28, 28, 45, 45, 28, 45, 45, 45, 45, 15, 15, 15, 5, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 28, 28, 28, 45, 45, 45, 15, 15, 15, 15, 3, 1, 3, 15, 15, 15, 15] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 205 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628723847 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 Building ZINC001628723847 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628723847 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 446) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001628723847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628723847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001628723847 none C[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 30, 30, 45, 45, 30, 45, 45, 45, 45, 16, 16, 16, 6, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 16, 16, 30, 30, 30, 45, 45, 45, 16, 16, 16, 16, 3, 3, 3, 16, 16, 16, 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]) total number of confs: 186 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 447) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001628723847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628723847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001628723847 none C[C@@H](c1ccc(F)cc1F)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 28, 28, 45, 45, 28, 45, 45, 45, 45, 15, 15, 15, 5, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 28, 28, 28, 45, 45, 45, 15, 15, 15, 15, 3, 1, 3, 15, 15, 15, 15] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 205 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628723847 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628723847 Building ZINC001628747904 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628747904 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/448 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CSCc2ccc(Br)cc21)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628747904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628747904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001628747904 none O=C(N[C@H]1CSCc2ccc(Br)cc21)[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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens need 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, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/449 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CSCc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628747904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628747904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001628747904 none O=C(N[C@H]1CSCc2ccc(Br)cc21)[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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens need 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, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628747904 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 Building ZINC001628747904 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628747904 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 448) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@H]1CSCc2ccc(Br)cc21)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628747904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628747904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001628747904 none O=C(N[C@H]1CSCc2ccc(Br)cc21)[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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens need 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, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 449) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@H]1CSCc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628747904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628747904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001628747904 none O=C(N[C@H]1CSCc2ccc(Br)cc21)[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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens need 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, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628747904 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747904 Building ZINC001628747905 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628747905 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/450 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CSCc2ccc(Br)cc21)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628747905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628747905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001628747905 none O=C(N[C@@H]1CSCc2ccc(Br)cc21)[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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens need 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, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 22, 22, 22, 22, 22, 22, 22, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/451 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CSCc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628747905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628747905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001628747905 none O=C(N[C@@H]1CSCc2ccc(Br)cc21)[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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens need 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, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 24, 24, 24, 24, 24, 24, 24, 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, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628747905 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 Building ZINC001628747905 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628747905 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 450) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@@H]1CSCc2ccc(Br)cc21)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628747905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628747905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001628747905 none O=C(N[C@@H]1CSCc2ccc(Br)cc21)[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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens need 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, 15, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 22, 22, 22, 22, 22, 22, 22, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 451) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@@H]1CSCc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001628747905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628747905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001628747905 none O=C(N[C@@H]1CSCc2ccc(Br)cc21)[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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 14, 5, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens need 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, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 24, 24, 24, 24, 24, 24, 24, 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, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628747905 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628747905 Building ZINC001628819888 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628819888 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/452 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628819888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628819888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001628819888 none O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[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', 'Cl', 'C.ar', 'Cl', '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, 5, 8, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 7, 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: [5, 2, 9, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 11, 11, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 2, 2] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/453 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628819888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628819888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001628819888 none O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[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', 'Cl', 'C.ar', 'Cl', '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, 5, 8, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 7, 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, 9, 11, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 11, 11, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 11, 11, 32, 32, 32, 11, 11, 11, 11, 2, 2] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628819888 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 Building ZINC001628819888 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628819888 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 452) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628819888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628819888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001628819888 none O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[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', 'Cl', 'C.ar', 'Cl', '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, 5, 8, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 7, 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: [5, 2, 9, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 11, 11, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 2, 2] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 453) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628819888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628819888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001628819888 none O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[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', 'Cl', 'C.ar', 'Cl', '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, 5, 8, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 7, 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, 9, 11, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 11, 11, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 11, 11, 32, 32, 32, 11, 11, 11, 11, 2, 2] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628819888 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628819888 Building ZINC001628877139 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628877139 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/454 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628877139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628877139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628877139 none O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 12, 3, 12, 12, 21, 29, 42, 46, 46, 46, 46, 46, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 12, 12, 5, 21, 21, 46, 46, 46, 46, 46, 46, 46, 46, 46, 12, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/455 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628877139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628877139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628877139 none O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 18, 25, 40, 46, 46, 46, 46, 46, 10, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 10, 10, 3, 18, 18, 46, 46, 46, 46, 46, 46, 46, 46, 46, 10, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628877139 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 Building ZINC001628877139 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628877139 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 454) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628877139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628877139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628877139 none O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 12, 3, 12, 12, 21, 29, 42, 46, 46, 46, 46, 46, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 12, 12, 5, 21, 21, 46, 46, 46, 46, 46, 46, 46, 46, 46, 12, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 455) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628877139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628877139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628877139 none O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 18, 25, 40, 46, 46, 46, 46, 46, 10, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 10, 10, 3, 18, 18, 46, 46, 46, 46, 46, 46, 46, 46, 46, 10, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628877139 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877139 Building ZINC001628877140 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628877140 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/456 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628877140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628877140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628877140 none O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 22, 31, 43, 47, 47, 47, 47, 47, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 11, 11, 5, 22, 22, 47, 47, 47, 47, 47, 47, 47, 47, 47, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/457 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628877140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628877140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628877140 none O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 12, 3, 12, 12, 21, 30, 41, 45, 45, 45, 45, 45, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 12, 12, 3, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 12, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628877140 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 Building ZINC001628877140 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628877140 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 456) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628877140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628877140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628877140 none O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 22, 31, 43, 47, 47, 47, 47, 47, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 11, 11, 5, 22, 22, 47, 47, 47, 47, 47, 47, 47, 47, 47, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 457) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001628877140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628877140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001628877140 none O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 12, 3, 12, 12, 21, 30, 41, 45, 45, 45, 45, 45, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 12, 12, 3, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 12, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628877140 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628877140 Building ZINC001628886897 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628886897 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/458 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 26, 26, 40, 40, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 26, 26, 40, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/459 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 26, 33, 40, 40, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 26, 26, 40, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/460 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/460' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 15, 27, 41, 41, 27, 27, 41, 41, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 3, 15, 15, 15, 15, 27, 27, 41, 41, 41, 41, 15, 15, 15, 15, 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/461 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/461' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 41, 41, 27, 34, 41, 41, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 27, 27, 41, 41, 41, 41, 14, 14, 14, 14, 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]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628886897 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 Building ZINC001628886897 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628886897 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 458) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 26, 26, 40, 40, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 26, 26, 40, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 459) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 26, 33, 40, 40, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 26, 26, 40, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 460) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 15, 27, 41, 41, 27, 27, 41, 41, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 3, 15, 15, 15, 15, 27, 27, 41, 41, 41, 41, 15, 15, 15, 15, 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 461) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 41, 41, 27, 34, 41, 41, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 27, 27, 41, 41, 41, 41, 14, 14, 14, 14, 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]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628886897 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 Building ZINC001628886897 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628886897 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 458) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 26, 26, 40, 40, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 26, 26, 40, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 459) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 26, 33, 40, 40, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 26, 26, 40, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 460) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 15, 27, 41, 41, 27, 27, 41, 41, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 3, 15, 15, 15, 15, 27, 27, 41, 41, 41, 41, 15, 15, 15, 15, 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 461) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 41, 41, 27, 34, 41, 41, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 27, 27, 41, 41, 41, 41, 14, 14, 14, 14, 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]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628886897 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 Building ZINC001628886897 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001628886897 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 458) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 26, 26, 40, 40, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 26, 26, 40, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 459) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 26, 40, 40, 26, 33, 40, 40, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 26, 26, 40, 40, 40, 40, 14, 14, 14, 14, 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 460) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 15, 27, 41, 41, 27, 27, 41, 41, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 3, 15, 15, 15, 15, 27, 27, 41, 41, 41, 41, 15, 15, 15, 15, 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 461) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001628886897.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001628886897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001628886897 none O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 27, 41, 41, 27, 34, 41, 41, 14, 14, 1, 1, 1, 7, 7, 7, 7, 7, 3, 14, 14, 14, 14, 27, 27, 41, 41, 41, 41, 14, 14, 14, 14, 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]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628886897 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628886897 Building ZINC001628895201 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628895201 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/462 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(c3ccc(F)cc3)c3ccc(F)cc3)CC2)c1) `ZINC001628895201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628895201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001628895201 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(c3ccc(F)cc3)c3ccc(F)cc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 5, 11, 11, 11, 11, 20, 22, 22, 20, 20, 22, 22, 20, 20, 20, 20, 20, 20, 20, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 20, 22, 22, 22, 22, 20, 20, 20, 20, 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, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/463 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(c3ccc(F)cc3)c3ccc(F)cc3)CC2)c1) `ZINC001628895201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628895201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001628895201 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(c3ccc(F)cc3)c3ccc(F)cc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 6, 15, 15, 15, 15, 23, 25, 25, 23, 23, 25, 25, 23, 24, 24, 23, 24, 24, 24, 15, 15, 6, 6, 6, 6, 2, 6, 6, 15, 15, 15, 15, 23, 25, 25, 25, 25, 24, 24, 24, 24, 15, 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, 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: 96 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628895201 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 Building ZINC001628895201 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628895201 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 462) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(c3ccc(F)cc3)c3ccc(F)cc3)CC2)c1) `ZINC001628895201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628895201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001628895201 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(c3ccc(F)cc3)c3ccc(F)cc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 5, 11, 11, 11, 11, 20, 22, 22, 20, 20, 22, 22, 20, 20, 20, 20, 20, 20, 20, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 20, 22, 22, 22, 22, 20, 20, 20, 20, 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, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 463) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(c3ccc(F)cc3)c3ccc(F)cc3)CC2)c1) `ZINC001628895201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628895201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001628895201 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(c3ccc(F)cc3)c3ccc(F)cc3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 1, 1, 1, 15, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 6, 6, 1, 1, 1, 1, 3, 6, 15, 15, 15, 15, 23, 25, 25, 23, 23, 25, 25, 23, 24, 24, 23, 24, 24, 24, 15, 15, 6, 6, 6, 6, 2, 6, 6, 15, 15, 15, 15, 23, 25, 25, 25, 25, 24, 24, 24, 24, 15, 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, 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: 96 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628895201 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628895201 Building ZINC001628896738 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628896738 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/464 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1) `ZINC001628896738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628896738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001628896738 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 22, 24, 12, 22, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 28, 47, 47, 47, 47, 47, 47, 47, 47, 47, 24, 24, 24, 12, 12, 2, 3, 1, 3, 28, 28, 47, 47, 47, 47, 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, 46, 47, 48]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/465 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1) `ZINC001628896738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628896738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001628896738 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 17, 19, 11, 17, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 16, 27, 46, 46, 46, 46, 46, 46, 46, 46, 46, 19, 19, 19, 11, 11, 2, 3, 1, 3, 27, 27, 46, 46, 46, 46, 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, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628896738 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 Building ZINC001628896738 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628896738 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 464) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1) `ZINC001628896738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628896738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001628896738 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 22, 24, 12, 22, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 28, 47, 47, 47, 47, 47, 47, 47, 47, 47, 24, 24, 24, 12, 12, 2, 3, 1, 3, 28, 28, 47, 47, 47, 47, 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, 46, 47, 48]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 465) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1) `ZINC001628896738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628896738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001628896738 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 17, 19, 11, 17, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 16, 27, 46, 46, 46, 46, 46, 46, 46, 46, 46, 19, 19, 19, 11, 11, 2, 3, 1, 3, 27, 27, 46, 46, 46, 46, 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, 46, 47, 48]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628896738 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896738 Building ZINC001628896739 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628896739 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/466 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1) `ZINC001628896739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628896739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001628896739 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 17, 19, 11, 17, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 16, 27, 47, 47, 47, 47, 47, 47, 47, 47, 47, 19, 19, 19, 11, 11, 2, 3, 1, 3, 27, 27, 47, 47, 47, 47, 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, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/467 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1) `ZINC001628896739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628896739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001628896739 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 23, 25, 12, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 29, 47, 47, 47, 47, 47, 47, 47, 47, 47, 25, 25, 25, 12, 12, 2, 3, 1, 3, 29, 29, 47, 47, 47, 47, 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, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628896739 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 Building ZINC001628896739 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628896739 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 466) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1) `ZINC001628896739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628896739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001628896739 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens 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, 17, 19, 11, 17, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 16, 27, 47, 47, 47, 47, 47, 47, 47, 47, 47, 19, 19, 19, 11, 11, 2, 3, 1, 3, 27, 27, 47, 47, 47, 47, 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, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 467) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1) `ZINC001628896739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628896739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001628896739 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)Cc1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 23, 25, 12, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 29, 47, 47, 47, 47, 47, 47, 47, 47, 47, 25, 25, 25, 12, 12, 2, 3, 1, 3, 29, 29, 47, 47, 47, 47, 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, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628896739 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628896739 Building ZINC001628978774 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628978774 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/468 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC001628978774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628978774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001628978774 none CCOc1ccc([C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 13, 12, 14, 14, 8, 8, 8, 8, 8, 8, 8, 12, 12, 15, 15, 15, 15, 8, 3, 8, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 14, 14, 15, 15, 15, 15, 15, 14, 14, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/469 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC001628978774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628978774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001628978774 none CCOc1ccc([C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 4, 4, 13, 13, 4, 4, 4, 4, 4, 4, 4, 9, 9, 12, 12, 12, 12, 4, 3, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 13, 13, 23, 23, 23, 23, 23, 13, 13, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13] 50 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628978774 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 Building ZINC001628978774 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001628978774 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 468) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC001628978774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001628978774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001628978774 none CCOc1ccc([C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 13, 12, 14, 14, 8, 8, 8, 8, 8, 8, 8, 12, 12, 15, 15, 15, 15, 8, 3, 8, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 14, 14, 15, 15, 15, 15, 15, 14, 14, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 469) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc([C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1) `ZINC001628978774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001628978774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001628978774 none CCOc1ccc([C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 4, 4, 13, 13, 4, 4, 4, 4, 4, 4, 4, 9, 9, 12, 12, 12, 12, 4, 3, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 13, 13, 23, 23, 23, 23, 23, 13, 13, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13] 50 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001628978774 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001628978774 Building ZINC001629081117 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629081117 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/470 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001629081117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629081117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001629081117 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 19, 35, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 14, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 1, 2, 19, 19] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/471 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001629081117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629081117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001629081117 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 19, 36, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 14, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 1, 2, 19, 19] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629081117 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 Building ZINC001629081117 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629081117 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 470) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001629081117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629081117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001629081117 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 19, 35, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 14, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 1, 2, 19, 19] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 471) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001629081117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629081117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001629081117 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 19, 36, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 14, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 1, 2, 19, 19] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629081117 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081117 Building ZINC001629081118 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629081118 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/472 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001629081118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629081118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001629081118 none CC(C)(C)OC(=O)N1CC[C@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 22, 38, 22, 22, 22, 22, 22, 22, 22, 22, 12, 1, 11, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 1, 2, 22, 22] 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/473 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001629081118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629081118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001629081118 none CC(C)(C)OC(=O)N1CC[C@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 11, 26, 11, 11, 11, 11, 11, 11, 11, 11, 9, 1, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 1, 2, 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629081118 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 Building ZINC001629081118 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629081118 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 472) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001629081118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629081118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001629081118 none CC(C)(C)OC(=O)N1CC[C@]2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 22, 38, 22, 22, 22, 22, 22, 22, 22, 22, 12, 1, 11, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 1, 2, 22, 22] 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 473) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001629081118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629081118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001629081118 none CC(C)(C)OC(=O)N1CC[C@]2(C1)CCCN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 11, 26, 11, 11, 11, 11, 11, 11, 11, 11, 9, 1, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 1, 2, 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629081118 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629081118 Building ZINC001629125026 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629125026 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/474 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 30, 30, 30, 30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 30, 30, 46, 46, 50, 50, 50, 50, 50, 38, 38, 30, 30, 30, 30, 9, 9, 2, 2, 1, 2, 30, 30, 30, 30, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/475 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 30, 30, 30, 30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 30, 30, 46, 46, 50, 50, 50, 50, 50, 38, 38, 30, 30, 30, 30, 9, 9, 2, 2, 1, 2, 30, 30, 30, 30, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/476 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/476' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 29, 29, 46, 46, 50, 50, 50, 50, 50, 38, 38, 29, 29, 29, 29, 9, 9, 2, 2, 1, 2, 29, 29, 29, 29, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/477 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/477' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 44, 36, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 29, 29, 44, 44, 50, 50, 50, 50, 50, 36, 36, 29, 29, 29, 29, 9, 9, 2, 2, 1, 2, 29, 29, 29, 29, 44] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629125026 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 Building ZINC001629125026 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629125026 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 474) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 30, 30, 30, 30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 30, 30, 46, 46, 50, 50, 50, 50, 50, 38, 38, 30, 30, 30, 30, 9, 9, 2, 2, 1, 2, 30, 30, 30, 30, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 475) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 30, 30, 30, 30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 30, 30, 46, 46, 50, 50, 50, 50, 50, 38, 38, 30, 30, 30, 30, 9, 9, 2, 2, 1, 2, 30, 30, 30, 30, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 476) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 29, 29, 46, 46, 50, 50, 50, 50, 50, 38, 38, 29, 29, 29, 29, 9, 9, 2, 2, 1, 2, 29, 29, 29, 29, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 477) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 44, 36, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 29, 29, 44, 44, 50, 50, 50, 50, 50, 36, 36, 29, 29, 29, 29, 9, 9, 2, 2, 1, 2, 29, 29, 29, 29, 44] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629125026 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 Building ZINC001629125026 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629125026 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 474) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 30, 30, 30, 30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 30, 30, 46, 46, 50, 50, 50, 50, 50, 38, 38, 30, 30, 30, 30, 9, 9, 2, 2, 1, 2, 30, 30, 30, 30, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 475) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 30, 30, 30, 30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 30, 30, 46, 46, 50, 50, 50, 50, 50, 38, 38, 30, 30, 30, 30, 9, 9, 2, 2, 1, 2, 30, 30, 30, 30, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 476) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 29, 29, 46, 46, 50, 50, 50, 50, 50, 38, 38, 29, 29, 29, 29, 9, 9, 2, 2, 1, 2, 29, 29, 29, 29, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 477) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 44, 36, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 29, 29, 44, 44, 50, 50, 50, 50, 50, 36, 36, 29, 29, 29, 29, 9, 9, 2, 2, 1, 2, 29, 29, 29, 29, 44] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629125026 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 Building ZINC001629125026 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629125026 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 474) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 30, 30, 30, 30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 30, 30, 46, 46, 50, 50, 50, 50, 50, 38, 38, 30, 30, 30, 30, 9, 9, 2, 2, 1, 2, 30, 30, 30, 30, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 475) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 30, 30, 30, 30, 14, 30, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 30, 30, 46, 46, 50, 50, 50, 50, 50, 38, 38, 30, 30, 30, 30, 9, 9, 2, 2, 1, 2, 30, 30, 30, 30, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 476) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 38, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 29, 29, 46, 46, 50, 50, 50, 50, 50, 38, 38, 29, 29, 29, 29, 9, 9, 2, 2, 1, 2, 29, 29, 29, 29, 46] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 477) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001629125026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629125026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001629125026 none CCc1nc(C[N@]2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', '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', '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'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 44, 36, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 29, 29, 44, 44, 50, 50, 50, 50, 50, 36, 36, 29, 29, 29, 29, 9, 9, 2, 2, 1, 2, 29, 29, 29, 29, 44] 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629125026 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629125026 Building ZINC001629164567 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629164567 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/478 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1F)Nc1cccc2c1CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001629164567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629164567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001629164567 none O=C(Nc1ccccc1F)Nc1cccc2c1CCCN2C(=O)[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', 'C.ar', 'C.ar', 'F', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 17, 19, 21, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1] 100 rigid atoms, others: [47, 48, 50, 51, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/479 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1F)Nc1cccc2c1CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001629164567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629164567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001629164567 none O=C(Nc1ccccc1F)Nc1cccc2c1CCCN2C(=O)[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', 'C.ar', 'C.ar', 'F', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 17, 19, 21, 50, 50, 23, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1] 100 rigid atoms, others: [47, 48, 50, 51, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629164567 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 Building ZINC001629164567 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629164567 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 478) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccccc1F)Nc1cccc2c1CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001629164567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629164567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001629164567 none O=C(Nc1ccccc1F)Nc1cccc2c1CCCN2C(=O)[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', 'C.ar', 'C.ar', 'F', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 17, 19, 21, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1] 100 rigid atoms, others: [47, 48, 50, 51, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 479) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccccc1F)Nc1cccc2c1CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001629164567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629164567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001629164567 none O=C(Nc1ccccc1F)Nc1cccc2c1CCCN2C(=O)[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', 'C.ar', 'C.ar', 'F', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 17, 19, 21, 50, 50, 23, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1] 100 rigid atoms, others: [47, 48, 50, 51, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629164567 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629164567 Building ZINC001629588596 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629588596 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/480 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 26, 24, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/481 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 26, 26, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/482 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/482' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 9, 9, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/483 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/483' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 13, 9, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 45, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629588596 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 Building ZINC001629588596 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629588596 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 480) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 26, 24, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 481) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 26, 26, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 482) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 9, 9, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 483) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 13, 9, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 45, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629588596 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 Building ZINC001629588596 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629588596 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 480) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 26, 24, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 481) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 26, 26, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 482) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 9, 9, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 483) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 13, 9, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 45, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629588596 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 Building ZINC001629588596 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629588596 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 480) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 26, 24, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 481) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 26, 26, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 482) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 9, 9, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 483) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1) `ZINC001629588596.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629588596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001629588596 none C[C@H]1CC[N@@](Cc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 13, 9, 26, 26, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 45, 26, 26, 9, 9, 2, 2, 2, 26, 26, 50, 50, 50, 50] 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]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629588596 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629588596 Building ZINC001629627685 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629627685 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/484 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1CCCNC(=O)OC(C)(C)C) `ZINC001629627685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629627685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001629627685 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1CCCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 14, 28, 37, 37, 38, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 14, 14, 28, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 139 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/485 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1CCCNC(=O)OC(C)(C)C) `ZINC001629627685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629627685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001629627685 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1CCCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 6, 6, 10, 28, 36, 36, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 6, 6, 6, 6, 10, 10, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629627685 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 Building ZINC001629627685 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629627685 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 484) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1CCCNC(=O)OC(C)(C)C) `ZINC001629627685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629627685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001629627685 none C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1CCCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 14, 28, 37, 37, 38, 38, 38, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 14, 14, 28, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 139 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 485) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1CCCNC(=O)OC(C)(C)C) `ZINC001629627685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629627685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001629627685 none C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1CCCNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 6, 6, 10, 28, 36, 36, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 6, 6, 6, 6, 10, 10, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629627685 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629627685 Building ZINC001629671654 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629671654 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/486 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3ccccc3OC(F)(F)F)C2)cc1Cl) `ZINC001629671654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629671654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001629671654 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3ccccc3OC(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 12, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 4, 4, 4, 10, 15, 15, 15, 15, 15, 15, 27, 28, 28, 28, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 10, 10, 15, 15, 15, 15, 4, 4, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/487 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3ccccc3OC(F)(F)F)C2)cc1Cl) `ZINC001629671654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629671654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001629671654 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3ccccc3OC(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 12, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 3, 3, 9, 13, 13, 12, 13, 13, 13, 27, 27, 27, 27, 3, 2, 2, 2, 4, 4, 4, 2, 2, 3, 3, 3, 9, 9, 13, 13, 13, 13, 3, 3, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629671654 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 Building ZINC001629671654 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629671654 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 486) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3ccccc3OC(F)(F)F)C2)cc1Cl) `ZINC001629671654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629671654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001629671654 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(Cc3ccccc3OC(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 12, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 4, 4, 4, 10, 15, 15, 15, 15, 15, 15, 27, 28, 28, 28, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 10, 10, 15, 15, 15, 15, 4, 4, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 487) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3ccccc3OC(F)(F)F)C2)cc1Cl) `ZINC001629671654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629671654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001629671654 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(Cc3ccccc3OC(F)(F)F)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 12, 5, 15, 15, 15, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 3, 3, 9, 13, 13, 12, 13, 13, 13, 27, 27, 27, 27, 3, 2, 2, 2, 4, 4, 4, 2, 2, 3, 3, 3, 9, 9, 13, 13, 13, 13, 3, 3, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629671654 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629671654 Building ZINC001629787416 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629787416 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/488 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2NS(=O)(=O)c2ccccc2F)cc1) `ZINC001629787416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629787416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001629787416 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2NS(=O)(=O)c2ccccc2F)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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 19, 32, 32, 32, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 6, 13, 13, 13, 19, 50, 50, 50, 50, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/489 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2NS(=O)(=O)c2ccccc2F)cc1) `ZINC001629787416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629787416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001629787416 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2NS(=O)(=O)c2ccccc2F)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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 20, 32, 32, 32, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 6, 14, 14, 14, 20, 50, 50, 50, 50, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629787416 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 Building ZINC001629787416 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629787416 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 488) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2NS(=O)(=O)c2ccccc2F)cc1) `ZINC001629787416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629787416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001629787416 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2NS(=O)(=O)c2ccccc2F)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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 19, 32, 32, 32, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 6, 13, 13, 13, 19, 50, 50, 50, 50, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 489) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2NS(=O)(=O)c2ccccc2F)cc1) `ZINC001629787416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629787416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001629787416 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2NS(=O)(=O)c2ccccc2F)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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 20, 32, 32, 32, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 6, 14, 14, 14, 20, 50, 50, 50, 50, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629787416 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629787416 Building ZINC001629810881 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629810881 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/490 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 19, 50, 50, 19, 19, 19, 19, 13, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 50, 50, 50, 50, 31, 50, 50, 19, 19, 19, 19, 12, 12, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 19, 19, 19, 19, 50] 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, 55, 56]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/491 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 13, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 12, 12, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/492 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/492' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 14, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 13, 13, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/493 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/493' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 14, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 13, 13, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629810881 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 Building ZINC001629810881 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629810881 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 490) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 19, 50, 50, 19, 19, 19, 19, 13, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 50, 50, 50, 50, 31, 50, 50, 19, 19, 19, 19, 12, 12, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 19, 19, 19, 19, 50] 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, 55, 56]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 491) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 13, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 12, 12, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 492) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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([N@]2CC[N@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 14, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 13, 13, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 493) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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([N@]2CC[N@@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 14, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 13, 13, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629810881 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 Building ZINC001629810881 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629810881 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 490) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 19, 50, 50, 19, 19, 19, 19, 13, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 50, 50, 50, 50, 31, 50, 50, 19, 19, 19, 19, 12, 12, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 19, 19, 19, 19, 50] 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, 55, 56]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 491) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 13, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 12, 12, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 492) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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([N@]2CC[N@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 14, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 13, 13, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 493) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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([N@]2CC[N@@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 14, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 13, 13, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629810881 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 Building ZINC001629810881 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629810881 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 490) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 19, 50, 50, 19, 19, 19, 19, 13, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 50, 50, 50, 50, 31, 50, 50, 19, 19, 19, 19, 12, 12, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 19, 19, 19, 19, 50] 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, 55, 56]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 491) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 13, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 12, 12, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 492) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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([N@]2CC[N@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 14, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 13, 13, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 493) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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([N@]2CC[N@@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001629810881.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629810881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001629810881 none Cc1cccc([N@]2CC[N@@](CCCCNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 20, 14, 10, 9, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 13, 13, 10, 10, 10, 10, 7, 7, 2, 2, 1, 2, 20, 20, 20, 20, 50] 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, 55, 56]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629810881 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629810881 Building ZINC001629991049 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629991049 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/494 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)c1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001629991049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629991049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001629991049 none CN(C[C@H](O)c1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 20, 33, 33, 33, 49, 49, 35, 49, 49, 49, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 20, 20, 99, 49, 49, 40, 49, 3, 1, 3] 150 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]) total number of confs: 316 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/495 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)c1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001629991049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629991049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001629991049 none CN(C[C@H](O)c1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 15, 32, 32, 32, 47, 47, 33, 47, 47, 47, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 15, 15, 96, 47, 47, 47, 47, 3, 1, 3] 150 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]) total number of confs: 320 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629991049 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 Building ZINC001629991049 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629991049 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 494) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C[C@H](O)c1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001629991049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629991049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001629991049 none CN(C[C@H](O)c1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 20, 33, 33, 33, 49, 49, 35, 49, 49, 49, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 20, 20, 99, 49, 49, 40, 49, 3, 1, 3] 150 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]) total number of confs: 316 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 495) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C[C@H](O)c1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001629991049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629991049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001629991049 none CN(C[C@H](O)c1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 15, 32, 32, 32, 47, 47, 33, 47, 47, 47, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 15, 15, 96, 47, 47, 47, 47, 3, 1, 3] 150 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]) total number of confs: 320 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629991049 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991049 Building ZINC001629991051 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629991051 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/496 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)c1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001629991051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629991051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001629991051 none CN(C[C@@H](O)c1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 16, 32, 32, 32, 49, 49, 32, 49, 49, 49, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 16, 16, 96, 49, 49, 34, 49, 3, 1, 3] 150 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]) total number of confs: 310 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/497 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)c1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001629991051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629991051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001629991051 none CN(C[C@@H](O)c1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 20, 34, 34, 34, 49, 49, 35, 49, 49, 49, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 20, 20, 102, 49, 49, 36, 49, 3, 1, 3] 150 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]) total number of confs: 310 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629991051 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 Building ZINC001629991051 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001629991051 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 496) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C[C@@H](O)c1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001629991051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629991051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001629991051 none CN(C[C@@H](O)c1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 16, 32, 32, 32, 49, 49, 32, 49, 49, 49, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 16, 16, 96, 49, 49, 34, 49, 3, 1, 3] 150 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]) total number of confs: 310 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 497) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C[C@@H](O)c1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001629991051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629991051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001629991051 none CN(C[C@@H](O)c1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 20, 34, 34, 34, 49, 49, 35, 49, 49, 49, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 20, 20, 102, 49, 49, 36, 49, 3, 1, 3] 150 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]) total number of confs: 310 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001629991051 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001629991051 Building ZINC001630048419 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630048419 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/498 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001630048419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630048419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001630048419 none COC(=O)c1cccc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 50, 33, 33, 33, 33, 10, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 33, 50, 50, 50, 33, 33, 33, 10, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 33] 50 rigid atoms, others: [41, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/499 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001630048419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630048419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001630048419 none COC(=O)c1cccc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 37, 37, 37, 37, 11, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 37, 50, 50, 50, 37, 37, 37, 11, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 37] 50 rigid atoms, others: [41, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 115 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630048419 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 Building ZINC001630048419 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630048419 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 498) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)c1cccc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001630048419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630048419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001630048419 none COC(=O)c1cccc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 50, 33, 33, 33, 33, 10, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 33, 50, 50, 50, 33, 33, 33, 10, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 33] 50 rigid atoms, others: [41, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 499) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)c1cccc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001630048419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630048419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001630048419 none COC(=O)c1cccc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 37, 37, 37, 37, 11, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 37, 50, 50, 50, 37, 37, 37, 11, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 37] 50 rigid atoms, others: [41, 42, 43, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 115 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630048419 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630048419 Building ZINC001630148915 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630148915 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/500 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CCC(=O)OC(C)(C)C)C1) `ZINC001630148915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630148915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001630148915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CCC(=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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 5, 6, 32, 32, 32, 32, 32, 32, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/501 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CCC(=O)OC(C)(C)C)C1) `ZINC001630148915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630148915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001630148915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CCC(=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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 9, 46, 46, 50, 50, 50, 50, 2, 2, 2, 2, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630148915 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 Building ZINC001630148915 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630148915 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 500) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CCC(=O)OC(C)(C)C)C1) `ZINC001630148915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630148915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001630148915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](CCC(=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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 5, 6, 32, 32, 32, 32, 32, 32, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 501) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CCC(=O)OC(C)(C)C)C1) `ZINC001630148915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630148915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001630148915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](CCC(=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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 9, 46, 46, 50, 50, 50, 50, 2, 2, 2, 2, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630148915 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148915 Building ZINC001630148920 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630148920 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/502 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CCC(=O)OC(C)(C)C)C1) `ZINC001630148920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630148920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001630148920 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CCC(=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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 8, 46, 46, 49, 49, 49, 49, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 8, 8, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/503 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CCC(=O)OC(C)(C)C)C1) `ZINC001630148920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630148920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001630148920 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CCC(=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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 3, 3, 5, 6, 33, 33, 36, 36, 36, 36, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630148920 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 Building ZINC001630148920 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630148920 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 502) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CCC(=O)OC(C)(C)C)C1) `ZINC001630148920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630148920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001630148920 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](CCC(=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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 8, 46, 46, 49, 49, 49, 49, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 8, 8, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 503) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CCC(=O)OC(C)(C)C)C1) `ZINC001630148920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630148920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001630148920 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](CCC(=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.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 3, 3, 5, 6, 33, 33, 36, 36, 36, 36, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630148920 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630148920 Building ZINC001630151455 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630151455 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/504 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](O)COc1cccc(Cl)c1Cl)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630151455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630151455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001630151455 none O=C(NC[C@@H](O)COc1cccc(Cl)c1Cl)[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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 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] 1 hydrogens 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, 10, 14, 14, 14, 20, 43, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 10, 10, 42, 20, 20, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/505 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](O)COc1cccc(Cl)c1Cl)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630151455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630151455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001630151455 none O=C(NC[C@@H](O)COc1cccc(Cl)c1Cl)[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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 9, 12, 12, 12, 22, 40, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 9, 9, 36, 22, 22, 49, 49, 49, 3, 1, 3] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630151455 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 Building ZINC001630151455 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630151455 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 504) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@@H](O)COc1cccc(Cl)c1Cl)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630151455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630151455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001630151455 none O=C(NC[C@@H](O)COc1cccc(Cl)c1Cl)[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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 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] 1 hydrogens 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, 10, 14, 14, 14, 20, 43, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 10, 10, 42, 20, 20, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 505) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@@H](O)COc1cccc(Cl)c1Cl)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630151455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630151455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001630151455 none O=C(NC[C@@H](O)COc1cccc(Cl)c1Cl)[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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 9, 12, 12, 12, 22, 40, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 9, 9, 36, 22, 22, 49, 49, 49, 3, 1, 3] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630151455 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151455 Building ZINC001630151456 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630151456 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/506 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](O)COc1cccc(Cl)c1Cl)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630151456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630151456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001630151456 none O=C(NC[C@H](O)COc1cccc(Cl)c1Cl)[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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 9, 12, 12, 12, 23, 41, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 9, 9, 36, 23, 23, 49, 49, 49, 3, 1, 3] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/507 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](O)COc1cccc(Cl)c1Cl)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630151456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630151456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001630151456 none O=C(NC[C@H](O)COc1cccc(Cl)c1Cl)[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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 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] 1 hydrogens 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, 10, 14, 14, 14, 20, 42, 50, 50, 49, 50, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 10, 10, 42, 20, 20, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630151456 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 Building ZINC001630151456 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630151456 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 506) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(NC[C@H](O)COc1cccc(Cl)c1Cl)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630151456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630151456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001630151456 none O=C(NC[C@H](O)COc1cccc(Cl)c1Cl)[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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 9, 12, 12, 12, 23, 41, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 9, 9, 36, 23, 23, 49, 49, 49, 3, 1, 3] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 507) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(NC[C@H](O)COc1cccc(Cl)c1Cl)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630151456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630151456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001630151456 none O=C(NC[C@H](O)COc1cccc(Cl)c1Cl)[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', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 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] 1 hydrogens 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, 10, 14, 14, 14, 20, 42, 50, 50, 49, 50, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 10, 10, 42, 20, 20, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630151456 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630151456 Building ZINC001630182807 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630182807 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/508 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl) `ZINC001630182807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630182807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182807 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 12, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 12, 23, 23, 23, 29, 29, 29, 23, 29, 29, 29, 12, 12, 12, 4, 11, 11, 69, 29, 23, 29] 150 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/509 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl) `ZINC001630182807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630182807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182807 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 15, 25, 25, 25, 28, 28, 28, 25, 28, 28, 28, 15, 15, 15, 5, 11, 11, 75, 28, 25, 28] 150 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630182807 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 Building ZINC001630182807 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630182807 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 508) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl) `ZINC001630182807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630182807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182807 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 12, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 12, 23, 23, 23, 29, 29, 29, 23, 29, 29, 29, 12, 12, 12, 4, 11, 11, 69, 29, 23, 29] 150 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 509) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl) `ZINC001630182807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630182807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182807 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 15, 25, 25, 25, 28, 28, 28, 25, 28, 28, 28, 15, 15, 15, 5, 11, 11, 75, 28, 25, 28] 150 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]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630182807 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182807 Building ZINC001630182808 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630182808 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/510 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl) `ZINC001630182808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630182808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182808 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 5, 14, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 14, 25, 25, 25, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 5, 10, 10, 75, 28, 28, 28] 150 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/511 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl) `ZINC001630182808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630182808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182808 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 12, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 12, 23, 23, 23, 28, 28, 28, 28, 28, 28, 28, 12, 12, 12, 4, 11, 11, 69, 28, 28, 28] 150 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630182808 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 Building ZINC001630182808 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630182808 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 510) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl) `ZINC001630182808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630182808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182808 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 5, 14, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 14, 25, 25, 25, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 5, 10, 10, 75, 28, 28, 28] 150 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 511) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl) `ZINC001630182808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630182808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182808 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 12, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 12, 23, 23, 23, 28, 28, 28, 28, 28, 28, 28, 12, 12, 12, 4, 11, 11, 69, 28, 28, 28] 150 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630182808 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182808 Building ZINC001630182809 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630182809 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/512 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl) `ZINC001630182809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630182809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182809 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 17, 34, 34, 34, 35, 35, 35, 34, 35, 35, 35, 17, 17, 17, 5, 10, 10, 102, 35, 34, 35] 150 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]) total number of confs: 254 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/513 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl) `ZINC001630182809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630182809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182809 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 5, 13, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 13, 5, 9, 9, 99, 33, 33, 33] 150 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]) total number of confs: 236 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630182809 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 Building ZINC001630182809 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630182809 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 512) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl) `ZINC001630182809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630182809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182809 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 17, 34, 34, 34, 35, 35, 35, 34, 35, 35, 35, 17, 17, 17, 5, 10, 10, 102, 35, 34, 35] 150 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]) total number of confs: 254 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 513) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl) `ZINC001630182809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630182809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182809 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens 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, 5, 13, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 13, 5, 9, 9, 99, 33, 33, 33] 150 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]) total number of confs: 236 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630182809 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182809 Building ZINC001630182810 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630182810 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/514 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl) `ZINC001630182810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630182810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182810 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 17, 5, 9, 9, 93, 31, 31, 31] 150 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]) total number of confs: 224 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/515 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl) `ZINC001630182810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630182810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182810 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 4, 17, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 17, 34, 34, 34, 35, 35, 35, 35, 35, 35, 35, 17, 17, 17, 4, 10, 10, 102, 35, 35, 35] 150 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]) total number of confs: 252 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630182810 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 Building ZINC001630182810 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630182810 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 514) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl) `ZINC001630182810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630182810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182810 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 17, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 17, 5, 9, 9, 93, 31, 31, 31] 150 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]) total number of confs: 224 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 515) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl) `ZINC001630182810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630182810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001630182810 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H](O)c1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 12, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 4, 17, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 17, 34, 34, 34, 35, 35, 35, 35, 35, 35, 35, 17, 17, 17, 4, 10, 10, 102, 35, 35, 35] 150 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]) total number of confs: 252 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630182810 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630182810 Building ZINC001630246560 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630246560 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/516 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCCN2CCCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630246560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630246560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001630246560 none O=C(Nc1ccc(OCCN2CCCCC2)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 20, 24, 24, 45, 45, 45, 45, 45, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 24, 24, 24, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/517 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCCN2CCCCC2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630246560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630246560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001630246560 none O=C(Nc1ccc(OCCN2CCCCC2)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 24, 24, 24, 45, 45, 45, 45, 45, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 24, 24, 24, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630246560 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 Building ZINC001630246560 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630246560 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 516) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccc(OCCN2CCCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630246560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630246560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001630246560 none O=C(Nc1ccc(OCCN2CCCCC2)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 20, 24, 24, 45, 45, 45, 45, 45, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 24, 24, 24, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 517) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccc(OCCN2CCCCC2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630246560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630246560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001630246560 none O=C(Nc1ccc(OCCN2CCCCC2)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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 24, 24, 24, 45, 45, 45, 45, 45, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 2, 4, 4, 24, 24, 24, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630246560 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630246560 Building ZINC001630687566 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630687566 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/518 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)Nc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1) `ZINC001630687566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630687566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630687566 none Cc1ccc(C(=O)Nc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)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', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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: [38, 34, 38, 38, 34, 34, 34, 29, 29, 29, 29, 29, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 38, 38, 38, 38, 38, 38, 38, 34, 29, 29, 29, 17, 17, 3, 4, 4, 4, 4, 29, 38, 38] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/519 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)Nc2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1) `ZINC001630687566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630687566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630687566 none Cc1ccc(C(=O)Nc2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)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', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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: [40, 40, 40, 40, 34, 34, 34, 29, 29, 29, 29, 29, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 40, 40, 40, 40, 40, 40, 40, 34, 29, 29, 29, 16, 16, 3, 4, 4, 4, 4, 29, 40, 40] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630687566 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 Building ZINC001630687566 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630687566 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 518) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(C(=O)Nc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1) `ZINC001630687566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630687566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630687566 none Cc1ccc(C(=O)Nc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)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', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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: [38, 34, 38, 38, 34, 34, 34, 29, 29, 29, 29, 29, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 38, 38, 38, 38, 38, 38, 38, 34, 29, 29, 29, 17, 17, 3, 4, 4, 4, 4, 29, 38, 38] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 519) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(C(=O)Nc2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)cc1) `ZINC001630687566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630687566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630687566 none Cc1ccc(C(=O)Nc2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)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', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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: [40, 40, 40, 40, 34, 34, 34, 29, 29, 29, 29, 29, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 40, 40, 40, 40, 40, 40, 40, 34, 29, 29, 29, 16, 16, 3, 4, 4, 4, 4, 29, 40, 40] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630687566 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630687566 Building ZINC001630695608 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630695608 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/520 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@](O)(c1ccc(Cl)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630695608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630695608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630695608 none O=C(NC[C@](O)(c1ccc(Cl)cc1)C(F)(F)F)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 19, 39, 39, 44, 44, 39, 41, 44, 44, 39, 39, 39, 39, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 19, 19, 117, 44, 44, 44, 44, 4, 2, 4] 150 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: 316 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/521 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@](O)(c1ccc(Cl)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630695608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630695608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630695608 none O=C(NC[C@](O)(c1ccc(Cl)cc1)C(F)(F)F)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 39, 39, 46, 46, 39, 39, 46, 46, 39, 39, 39, 39, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 16, 16, 117, 46, 46, 46, 46, 4, 1, 4] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 317 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630695608 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 Building ZINC001630695608 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630695608 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 520) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@](O)(c1ccc(Cl)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630695608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630695608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630695608 none O=C(NC[C@](O)(c1ccc(Cl)cc1)C(F)(F)F)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 19, 39, 39, 44, 44, 39, 41, 44, 44, 39, 39, 39, 39, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 19, 19, 117, 44, 44, 44, 44, 4, 2, 4] 150 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: 316 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 521) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@](O)(c1ccc(Cl)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630695608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630695608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630695608 none O=C(NC[C@](O)(c1ccc(Cl)cc1)C(F)(F)F)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 39, 39, 46, 46, 39, 39, 46, 46, 39, 39, 39, 39, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 16, 16, 117, 46, 46, 46, 46, 4, 1, 4] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 317 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630695608 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695608 Building ZINC001630695609 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630695609 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/522 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@](O)(c1ccc(Cl)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630695609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630695609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630695609 none O=C(NC[C@@](O)(c1ccc(Cl)cc1)C(F)(F)F)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 38, 38, 45, 45, 38, 38, 45, 45, 38, 38, 38, 38, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 16, 16, 114, 45, 45, 45, 45, 4, 2, 4] 150 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: 313 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/523 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@](O)(c1ccc(Cl)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630695609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630695609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630695609 none O=C(NC[C@@](O)(c1ccc(Cl)cc1)C(F)(F)F)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 19, 39, 39, 44, 44, 39, 39, 44, 44, 39, 39, 39, 39, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 19, 19, 117, 44, 44, 44, 44, 4, 1, 4] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 310 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630695609 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 Building ZINC001630695609 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630695609 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 522) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@@](O)(c1ccc(Cl)cc1)C(F)(F)F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630695609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630695609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630695609 none O=C(NC[C@@](O)(c1ccc(Cl)cc1)C(F)(F)F)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 38, 38, 45, 45, 38, 38, 45, 45, 38, 38, 38, 38, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 16, 16, 114, 45, 45, 45, 45, 4, 2, 4] 150 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: 313 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 523) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NC[C@@](O)(c1ccc(Cl)cc1)C(F)(F)F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001630695609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630695609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630695609 none O=C(NC[C@@](O)(c1ccc(Cl)cc1)C(F)(F)F)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 19, 39, 39, 44, 44, 39, 39, 44, 44, 39, 39, 39, 39, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 19, 19, 117, 44, 44, 44, 44, 4, 1, 4] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 310 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630695609 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630695609 Building ZINC001630748549 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630748549 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/524 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)OCO2) `ZINC001630748549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630748549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630748549 none CC(C)(C)OC(=O)Nc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)OCO2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 29, 14, 14, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 21, 14, 14, 3, 4, 4, 4, 4, 14, 14] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/525 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)OCO2) `ZINC001630748549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630748549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630748549 none CC(C)(C)OC(=O)Nc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)OCO2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 29, 14, 14, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 14, 14, 3, 4, 4, 4, 4, 14, 14] 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630748549 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 Building ZINC001630748549 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630748549 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 524) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)Nc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)OCO2) `ZINC001630748549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630748549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630748549 none CC(C)(C)OC(=O)Nc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)OCO2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 29, 14, 14, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 21, 14, 14, 3, 4, 4, 4, 4, 14, 14] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 525) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)Nc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)OCO2) `ZINC001630748549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630748549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630748549 none CC(C)(C)OC(=O)Nc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)OCO2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 29, 14, 14, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 14, 14, 3, 4, 4, 4, 4, 14, 14] 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630748549 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630748549 Building ZINC001630816846 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630816846 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/526 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/526' -> `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])c1c[nH]c2cc(F)ccc21) `ZINC001630816846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630816846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001630816846 none O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.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, 8, 1, 1, 1, 1, 1, 17, 14, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 32, 32, 8, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/527 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/527' -> `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])c1c[nH]c2cc(F)ccc21) `ZINC001630816846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630816846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001630816846 none O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.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, 8, 1, 1, 1, 1, 1, 17, 14, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 8, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 32, 32, 8, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630816846 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 Building ZINC001630816846 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630816846 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 526) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001630816846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630816846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001630816846 none O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.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, 8, 1, 1, 1, 1, 1, 17, 14, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 32, 32, 8, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 527) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001630816846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630816846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001630816846 none O=C(Nc1cnc(c2ccc(Br)s2)nc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'N.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, 8, 1, 1, 1, 1, 1, 17, 14, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 8, 32, 32, 32, 32, 32, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 32, 32, 8, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630816846 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630816846 Building ZINC001630879002 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630879002 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/528 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630879002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630879002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630879002 none O=C(N1CC(Cc2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 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, 4, 13, 13, 13, 30, 36, 36, 32, 36, 36, 36, 36, 36, 36, 13, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 13, 30, 30, 36, 36, 36, 36, 13, 13, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/529 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630879002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630879002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630879002 none O=C(N1CC(Cc2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 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, 4, 14, 14, 14, 32, 38, 38, 37, 38, 38, 38, 38, 38, 38, 14, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 14, 32, 32, 38, 38, 38, 38, 14, 14, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630879002 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 Building ZINC001630879002 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630879002 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 528) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CC(Cc2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630879002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630879002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630879002 none O=C(N1CC(Cc2ccc(C(F)(F)F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 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, 4, 13, 13, 13, 30, 36, 36, 32, 36, 36, 36, 36, 36, 36, 13, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 13, 30, 30, 36, 36, 36, 36, 13, 13, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 529) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CC(Cc2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630879002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630879002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630879002 none O=C(N1CC(Cc2ccc(C(F)(F)F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 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, 4, 14, 14, 14, 32, 38, 38, 37, 38, 38, 38, 38, 38, 38, 14, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 14, 32, 32, 38, 38, 38, 38, 14, 14, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630879002 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630879002 Building ZINC001630960601 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630960601 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/530 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C) `ZINC001630960601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630960601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001630960601 none CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 25, 39, 39, 49, 49, 49, 49, 25, 25, 25, 15, 15, 6, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/531 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C) `ZINC001630960601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630960601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001630960601 none CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 6, 6, 6, 6, 6, 4, 2, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 21, 34, 34, 48, 48, 48, 48, 21, 21, 21, 13, 13, 6, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 155 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630960601 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 Building ZINC001630960601 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630960601 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 530) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C) `ZINC001630960601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630960601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001630960601 none CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 25, 39, 39, 49, 49, 49, 49, 25, 25, 25, 15, 15, 6, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 531) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C) `ZINC001630960601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630960601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001630960601 none CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 6, 6, 6, 6, 6, 4, 2, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 21, 34, 34, 48, 48, 48, 48, 21, 21, 21, 13, 13, 6, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 155 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630960601 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960601 Building ZINC001630960602 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630960602 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/532 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C) `ZINC001630960602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630960602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001630960602 none CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 22, 37, 37, 47, 47, 47, 47, 22, 22, 22, 14, 14, 6, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 163 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/533 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C) `ZINC001630960602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630960602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001630960602 none CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 25, 38, 38, 50, 50, 50, 50, 25, 25, 25, 15, 15, 6, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630960602 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 Building ZINC001630960602 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630960602 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 532) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C) `ZINC001630960602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630960602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001630960602 none CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 5, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 22, 37, 37, 47, 47, 47, 47, 22, 22, 22, 14, 14, 6, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 163 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 533) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C) `ZINC001630960602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630960602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001630960602 none CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 25, 38, 38, 50, 50, 50, 50, 25, 25, 25, 15, 15, 6, 6, 6, 6, 6, 6, 3, 1, 3, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630960602 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630960602 Building ZINC001630992280 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630992280 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/534 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)[C@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001630992280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630992280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001630992280 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)[C@H](C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 11, 11, 5, 11, 11, 5, 5, 5, 23, 23, 23, 23, 23, 23, 5, 2, 2, 2, 6, 6, 6, 2, 2, 5, 5, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/535 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)[C@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001630992280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630992280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001630992280 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)[C@H](C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 2, 4, 4, 4, 4, 7, 7, 5, 7, 7, 4, 4, 4, 23, 23, 26, 26, 26, 26, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630992280 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 Building ZINC001630992280 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630992280 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 534) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)[C@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001630992280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630992280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001630992280 none COc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)[C@H](C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 11, 11, 5, 11, 11, 5, 5, 5, 23, 23, 23, 23, 23, 23, 5, 2, 2, 2, 6, 6, 6, 2, 2, 5, 5, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 97 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 535) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)[C@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001630992280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630992280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001630992280 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3)[C@H](C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 2, 4, 4, 4, 4, 7, 7, 5, 7, 7, 4, 4, 4, 23, 23, 26, 26, 26, 26, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630992280 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630992280 Building ZINC001630993806 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630993806 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/536 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001630993806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630993806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001630993806 none COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 7, 9, 7, 7, 7, 7, 7, 13, 26, 33, 33, 27, 33, 33, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 9, 9, 9, 7, 7, 26, 26, 33, 33, 33, 33, 33, 3, 4, 4, 4, 4, 7] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/537 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001630993806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630993806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001630993806 none COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 8, 10, 8, 8, 8, 8, 8, 14, 26, 33, 33, 31, 33, 33, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 10, 10, 10, 8, 8, 26, 26, 33, 33, 33, 33, 33, 3, 4, 4, 4, 4, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630993806 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 Building ZINC001630993806 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630993806 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 536) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001630993806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630993806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001630993806 none COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 7, 9, 7, 7, 7, 7, 7, 13, 26, 33, 33, 27, 33, 33, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 9, 9, 9, 7, 7, 26, 26, 33, 33, 33, 33, 33, 3, 4, 4, 4, 4, 7] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 537) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001630993806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630993806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001630993806 none COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 8, 10, 8, 8, 8, 8, 8, 14, 26, 33, 33, 31, 33, 33, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 10, 10, 10, 8, 8, 26, 26, 33, 33, 33, 33, 33, 3, 4, 4, 4, 4, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001630993806 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001630993806 Building ZINC001631092765 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631092765 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/538 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001631092765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631092765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001631092765 none O=C(NCC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 38, 38, 33, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 38, 38, 33, 38, 23, 23, 23, 23, 23, 23, 23, 23, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/539 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001631092765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631092765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001631092765 none O=C(NCC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 34, 34, 30, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 34, 34, 30, 34, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631092765 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 Building ZINC001631092765 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631092765 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 538) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(NCC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001631092765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631092765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001631092765 none O=C(NCC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 38, 38, 33, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 23, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 38, 38, 33, 38, 23, 23, 23, 23, 23, 23, 23, 23, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 539) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(NCC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001631092765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631092765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001631092765 none O=C(NCC1(c2cccc(C(F)(F)F)c2)CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 34, 34, 30, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 34, 34, 30, 34, 19, 19, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631092765 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631092765 Building ZINC001631143130 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631143130 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/540 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001631143130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631143130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001631143130 none CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)OC(C)(C)C)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 5, 5, 8, 8, 12, 12, 12, 12, 5, 5, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/541 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001631143130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631143130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001631143130 none CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)OC(C)(C)C)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 9, 9, 14, 15, 15, 15, 6, 6, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631143130 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 Building ZINC001631143130 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631143130 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 540) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001631143130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631143130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001631143130 none CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)OC(C)(C)C)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 5, 5, 5, 5, 8, 8, 12, 12, 12, 12, 5, 5, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 541) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001631143130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631143130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001631143130 none CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCN(C(=O)OC(C)(C)C)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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 9, 9, 14, 15, 15, 15, 6, 6, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631143130 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631143130 Building ZINC001631200724 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631200724 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/542 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/542' -> `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](c1ccccc1)C1(CO)CCCC1) `ZINC001631200724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631200724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631200724 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)C1(CO)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 15, 24, 29, 24, 24, 24, 24, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 6, 9, 9, 9, 9, 9, 29, 29, 87, 24, 24, 24, 24, 24, 24, 24, 24] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 209 number of broken/clashed sets: 106 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/543 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/543' -> `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](c1ccccc1)C1(CO)CCCC1) `ZINC001631200724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631200724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631200724 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)C1(CO)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 19, 28, 35, 28, 28, 28, 28, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 6, 10, 10, 10, 10, 10, 35, 35, 105, 28, 28, 28, 28, 28, 28, 28, 28] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 241 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631200724 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 Building ZINC001631200724 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631200724 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 542) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)C1(CO)CCCC1) `ZINC001631200724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631200724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631200724 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)C1(CO)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 15, 24, 29, 24, 24, 24, 24, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 6, 9, 9, 9, 9, 9, 29, 29, 87, 24, 24, 24, 24, 24, 24, 24, 24] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 209 number of broken/clashed sets: 106 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 543) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)C1(CO)CCCC1) `ZINC001631200724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631200724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631200724 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)C1(CO)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 19, 28, 35, 28, 28, 28, 28, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 6, 10, 10, 10, 10, 10, 35, 35, 105, 28, 28, 28, 28, 28, 28, 28, 28] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 241 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631200724 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200724 Building ZINC001631200725 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631200725 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/544 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/544' -> `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](c1ccccc1)C1(CO)CCCC1) `ZINC001631200725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631200725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631200725 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)C1(CO)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 14, 27, 38, 27, 27, 27, 27, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 8, 8, 8, 8, 8, 38, 38, 114, 27, 27, 27, 27, 27, 27, 27, 27] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 269 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/545 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/545' -> `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](c1ccccc1)C1(CO)CCCC1) `ZINC001631200725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631200725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631200725 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)C1(CO)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 12, 26, 35, 26, 26, 26, 26, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 6, 8, 8, 8, 8, 8, 35, 35, 105, 26, 26, 26, 26, 26, 26, 26, 26] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 248 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631200725 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 Building ZINC001631200725 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631200725 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 544) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)C1(CO)CCCC1) `ZINC001631200725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631200725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631200725 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)C1(CO)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 14, 27, 38, 27, 27, 27, 27, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 8, 8, 8, 8, 8, 38, 38, 114, 27, 27, 27, 27, 27, 27, 27, 27] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 269 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 545) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)C1(CO)CCCC1) `ZINC001631200725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631200725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631200725 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)C1(CO)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 12, 26, 35, 26, 26, 26, 26, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 6, 8, 8, 8, 8, 8, 35, 35, 105, 26, 26, 26, 26, 26, 26, 26, 26] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 248 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631200725 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631200725 Building ZINC001631334408 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631334408 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/546 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001631334408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631334408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001631334408 none CC(C)(C)c1nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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] 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: [47, 43, 47, 47, 43, 43, 21, 7, 7, 7, 7, 4, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 43, 43, 47, 47, 47, 47, 47, 47, 47, 47, 47, 21, 21, 7, 7, 7, 7, 3, 1, 3, 7, 7, 7, 7, 43] 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/547 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001631334408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631334408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001631334408 none CC(C)(C)c1nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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] 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: [50, 49, 50, 50, 49, 49, 19, 7, 7, 7, 7, 4, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 7, 7, 7, 7, 3, 1, 3, 7, 7, 7, 7, 49] 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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631334408 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 Building ZINC001631334408 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631334408 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 546) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)c1nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001631334408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631334408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001631334408 none CC(C)(C)c1nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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] 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: [47, 43, 47, 47, 43, 43, 21, 7, 7, 7, 7, 4, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 43, 43, 47, 47, 47, 47, 47, 47, 47, 47, 47, 21, 21, 7, 7, 7, 7, 3, 1, 3, 7, 7, 7, 7, 43] 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 547) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)c1nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1) `ZINC001631334408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631334408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001631334408 none CC(C)(C)c1nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 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] 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: [50, 49, 50, 50, 49, 49, 19, 7, 7, 7, 7, 4, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 7, 7, 7, 7, 3, 1, 3, 7, 7, 7, 7, 49] 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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631334408 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631334408 Building ZINC001631414260 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631414260 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/548 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccccc2Br)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631414260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631414260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001631414260 none O=C(N1CC(Cc2ccccc2Br)C1)[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', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7, 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, 4, 13, 13, 13, 29, 39, 39, 35, 39, 39, 39, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 29, 29, 39, 39, 36, 39, 13, 13, 3, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/549 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccccc2Br)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631414260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631414260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001631414260 none O=C(N1CC(Cc2ccccc2Br)C1)[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', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7, 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, 4, 12, 12, 12, 27, 40, 40, 37, 40, 40, 40, 12, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 27, 27, 40, 40, 40, 40, 12, 12, 3, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631414260 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 Building ZINC001631414260 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631414260 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 548) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CC(Cc2ccccc2Br)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631414260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631414260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001631414260 none O=C(N1CC(Cc2ccccc2Br)C1)[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', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7, 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, 4, 13, 13, 13, 29, 39, 39, 35, 39, 39, 39, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 29, 29, 39, 39, 36, 39, 13, 13, 3, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 549) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CC(Cc2ccccc2Br)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631414260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631414260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001631414260 none O=C(N1CC(Cc2ccccc2Br)C1)[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', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7, 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, 4, 12, 12, 12, 27, 40, 40, 37, 40, 40, 40, 12, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 27, 27, 40, 40, 40, 40, 12, 12, 3, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631414260 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631414260 Building ZINC001631422326 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631422326 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/550 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/550' -> `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)NCCc1c[nH]c2cc(F)c(Cl)cc12) `ZINC001631422326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631422326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631422326 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)c(Cl)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.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 8, 6, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 13, 13, 26, 26, 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]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/551 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/551' -> `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)NCCc1c[nH]c2cc(F)c(Cl)cc12) `ZINC001631422326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631422326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631422326 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)c(Cl)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.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 8, 6, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 27, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 13, 13, 27, 27, 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]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631422326 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 Building ZINC001631422326 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631422326 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 550) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)c(Cl)cc12) `ZINC001631422326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631422326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631422326 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)c(Cl)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.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 8, 6, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 26, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 13, 13, 26, 26, 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]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 551) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)c(Cl)cc12) `ZINC001631422326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631422326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001631422326 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)c(Cl)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.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 8, 6, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 27, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 13, 13, 27, 27, 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]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631422326 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631422326 Building ZINC001631537247 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631537247 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/552 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001631537247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631537247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631537247 none CN(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 6, 23, 23, 12, 23, 23, 23, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 4, 7, 7, 23, 23, 12, 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]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/553 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001631537247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631537247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631537247 none CN(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 7, 26, 26, 14, 26, 26, 26, 26, 26, 26, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 26, 26, 14, 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: 129 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631537247 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 Building ZINC001631537247 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631537247 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 552) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001631537247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631537247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631537247 none CN(C)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 6, 23, 23, 12, 23, 23, 23, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 4, 7, 7, 23, 23, 12, 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]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 553) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001631537247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631537247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631537247 none CN(C)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 7, 26, 26, 14, 26, 26, 26, 26, 26, 26, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 26, 26, 14, 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: 129 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631537247 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537247 Building ZINC001631537248 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631537248 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/554 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001631537248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631537248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631537248 none CN(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 6, 24, 24, 12, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 24, 24, 12, 24] 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: 121 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/555 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001631537248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631537248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631537248 none CN(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 6, 23, 23, 12, 23, 23, 23, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 4, 7, 7, 23, 23, 12, 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]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631537248 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 Building ZINC001631537248 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631537248 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 554) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001631537248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631537248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631537248 none CN(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 6, 24, 24, 12, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 24, 24, 12, 24] 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: 121 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 555) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1) `ZINC001631537248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631537248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631537248 none CN(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 4, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 6, 23, 23, 12, 23, 23, 23, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 4, 7, 7, 23, 23, 12, 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]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631537248 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631537248 Building ZINC001631577450 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631577450 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/556 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1csc(c2ccccc2)n1) `ZINC001631577450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631577450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001631577450 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1csc(c2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 14, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 25, 36, 36, 36, 36, 39, 39, 37, 39, 39, 36, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 16, 16, 25, 25, 36, 39, 39, 37, 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]) total number of confs: 150 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/557 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1csc(c2ccccc2)n1) `ZINC001631577450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631577450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001631577450 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1csc(c2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 14, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 15, 23, 36, 36, 36, 36, 39, 39, 37, 39, 39, 36, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 3, 15, 15, 23, 23, 36, 39, 39, 37, 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]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631577450 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 Building ZINC001631577450 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631577450 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 556) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1csc(c2ccccc2)n1) `ZINC001631577450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631577450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001631577450 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1csc(c2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 14, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 25, 36, 36, 36, 36, 39, 39, 37, 39, 39, 36, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 16, 16, 25, 25, 36, 39, 39, 37, 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]) total number of confs: 150 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 557) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1csc(c2ccccc2)n1) `ZINC001631577450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631577450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001631577450 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1csc(c2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 14, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 15, 23, 36, 36, 36, 36, 39, 39, 37, 39, 39, 36, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 3, 15, 15, 23, 23, 36, 39, 39, 37, 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]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631577450 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631577450 Building ZINC001631714364 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631714364 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/558 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/558' -> `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(I)cc2)cs1) `ZINC001631714364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631714364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001631714364 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(I)cc2)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', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 18, 1, 1, 1, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 1, 4, 4, 4, 8, 8, 8, 18, 18, 15, 18, 18, 18, 8, 8, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 4, 18, 18, 18, 18, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/559 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/559' -> `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(I)cc2)cs1) `ZINC001631714364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631714364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001631714364 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(I)cc2)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', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 18, 1, 1, 1, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 1, 4, 4, 4, 8, 8, 8, 18, 18, 8, 12, 18, 18, 8, 8, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 4, 18, 18, 18, 18, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631714364 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 Building ZINC001631714364 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631714364 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 558) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(I)cc2)cs1) `ZINC001631714364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631714364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001631714364 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(I)cc2)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', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 18, 1, 1, 1, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 1, 4, 4, 4, 8, 8, 8, 18, 18, 15, 18, 18, 18, 8, 8, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 4, 18, 18, 18, 18, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 559) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(I)cc2)cs1) `ZINC001631714364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631714364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001631714364 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(I)cc2)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', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 18, 1, 1, 1, 14, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 1, 4, 4, 4, 8, 8, 8, 18, 18, 8, 12, 18, 18, 8, 8, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 4, 18, 18, 18, 18, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631714364 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631714364 Building ZINC001631827318 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631827318 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/560 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cn1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001631827318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631827318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631827318 none O=C(Nc1ccc(Cl)cn1)c1ccccc1NC(=O)[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', 'Cl', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 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] 0 hydrogens 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, 9, 23, 23, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 25, 25, 25, 9, 9, 9, 9, 3, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/561 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cn1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001631827318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631827318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631827318 none O=C(Nc1ccc(Cl)cn1)c1ccccc1NC(=O)[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', 'Cl', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 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] 0 hydrogens 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, 9, 23, 23, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 25, 25, 25, 9, 9, 9, 9, 3, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631827318 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 Building ZINC001631827318 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631827318 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 560) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccc(Cl)cn1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001631827318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631827318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631827318 none O=C(Nc1ccc(Cl)cn1)c1ccccc1NC(=O)[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', 'Cl', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 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] 0 hydrogens 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, 9, 23, 23, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 25, 25, 25, 9, 9, 9, 9, 3, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 561) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccc(Cl)cn1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001631827318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631827318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631827318 none O=C(Nc1ccc(Cl)cn1)c1ccccc1NC(=O)[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', 'Cl', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 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] 0 hydrogens 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, 9, 23, 23, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 25, 25, 25, 9, 9, 9, 9, 3, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631827318 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631827318 Building ZINC001631848861 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631848861 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/562 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1NC(=O)c1c(C)[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001631848861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631848861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001631848861 none COc1ccccc1NC(=O)c1c(C)[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', '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, 11, 1, 1, 5, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 36, 31, 36, 36, 19, 19, 12, 19, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 41, 41, 41, 36, 36, 36, 36, 19, 12, 12, 12, 4, 3, 1, 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]) total number of confs: 111 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/563 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1NC(=O)c1c(C)[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001631848861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631848861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001631848861 none COc1ccccc1NC(=O)c1c(C)[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', '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, 11, 1, 1, 5, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 36, 30, 36, 36, 19, 19, 12, 19, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 42, 42, 42, 36, 36, 36, 36, 19, 12, 12, 12, 4, 3, 1, 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]) total number of confs: 118 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631848861 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 Building ZINC001631848861 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631848861 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 562) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1NC(=O)c1c(C)[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001631848861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631848861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001631848861 none COc1ccccc1NC(=O)c1c(C)[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', '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, 11, 1, 1, 5, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 36, 31, 36, 36, 19, 19, 12, 19, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 41, 41, 41, 36, 36, 36, 36, 19, 12, 12, 12, 4, 3, 1, 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]) total number of confs: 111 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 563) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1NC(=O)c1c(C)[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001631848861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631848861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001631848861 none COc1ccccc1NC(=O)c1c(C)[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', '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, 11, 1, 1, 5, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 36, 30, 36, 36, 19, 19, 12, 19, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 42, 42, 42, 36, 36, 36, 36, 19, 12, 12, 12, 4, 3, 1, 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]) total number of confs: 118 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631848861 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631848861 Building ZINC001631863807 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631863807 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/564 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631863807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631863807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631863807 none CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [34, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 21, 21, 21, 21, 13, 13, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/565 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631863807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631863807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631863807 none CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631863807 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 Building ZINC001631863807 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631863807 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 564) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631863807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631863807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631863807 none CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [34, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 21, 21, 21, 21, 13, 13, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 565) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631863807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631863807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631863807 none CCn1c2ccccc2nc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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, 24, 24, 24, 24, 24, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631863807 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863807 Building ZINC001631863808 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631863808 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/566 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631863808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631863808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631863808 none CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/567 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631863808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631863808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631863808 none CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [32, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 21, 21, 21, 21, 13, 13, 13, 13, 13, 13, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631863808 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 Building ZINC001631863808 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631863808 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 566) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631863808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631863808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631863808 none CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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, 26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 33, 33, 33, 33, 33, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 567) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001631863808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631863808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001631863808 none CCn1c2ccccc2nc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [32, 21, 21, 21, 21, 21, 21, 21, 21, 21, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 21, 21, 21, 21, 13, 13, 13, 13, 13, 13, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631863808 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631863808 Building ZINC001631922850 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631922850 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/568 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/568' -> `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(Br)c2)n1) `ZINC001631922850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631922850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631922850 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(Br)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', 'Br', '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, 17, 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] 0 hydrogens 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, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 20, 20, 20, 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]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/569 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/569' -> `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(Br)c2)n1) `ZINC001631922850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631922850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631922850 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(Br)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', 'Br', '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, 17, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 19, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 6, 7, 7, 7, 7, 19, 19, 19, 19] 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: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631922850 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 Building ZINC001631922850 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631922850 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 568) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(Br)c2)n1) `ZINC001631922850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631922850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631922850 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(Br)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', 'Br', '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, 17, 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] 0 hydrogens 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, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 20, 20, 20, 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]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 569) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(Br)c2)n1) `ZINC001631922850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631922850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631922850 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n(c2cccc(Br)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', 'Br', '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, 17, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 19, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 6, 7, 7, 7, 7, 19, 19, 19, 19] 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: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001631922850 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001631922850 Building ZINC001632010067 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010067 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/570 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 19, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/571 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 19, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/572 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/572' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 13, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 13, 13, 3, 6, 6, 6, 6, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/573 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/573' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 13, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 13, 13, 3, 6, 6, 6, 6, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010067 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 Building ZINC001632010067 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010067 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 570) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 19, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 571) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 19, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 572) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 13, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 13, 13, 3, 6, 6, 6, 6, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 573) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 13, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 13, 13, 3, 6, 6, 6, 6, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010067 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 Building ZINC001632010067 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010067 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 570) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 19, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 571) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 19, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 572) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 13, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 13, 13, 3, 6, 6, 6, 6, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 573) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 13, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 13, 13, 3, 6, 6, 6, 6, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010067 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 Building ZINC001632010067 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010067 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 570) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 19, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 571) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 19, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 11, 11, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 572) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 13, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 13, 13, 3, 6, 6, 6, 6, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 573) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010067 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 13, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 13, 13, 3, 6, 6, 6, 6, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010067 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010067 Building ZINC001632010074 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010074 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/574 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 33, 33, 33] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/575 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 33, 33, 33] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/576 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/576' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/577 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/577' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010074 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 Building ZINC001632010074 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010074 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 574) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 33, 33, 33] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 575) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 33, 33, 33] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 576) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 577) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010074 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 Building ZINC001632010074 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010074 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 574) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 33, 33, 33] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 575) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 33, 33, 33] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 576) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 577) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010074 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 Building ZINC001632010074 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010074 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 574) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 33, 33, 33] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 575) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 33, 33, 33, 33, 33, 33, 33, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 33, 33, 33] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 576) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 577) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010074 none CN1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010074 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010074 Building ZINC001632010076 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010076 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/578 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/579 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/580 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/580' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/581 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/581' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010076 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 Building ZINC001632010076 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010076 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 578) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 579) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 580) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 581) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010076 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 Building ZINC001632010076 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010076 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 578) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 579) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 580) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 581) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010076 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 Building ZINC001632010076 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010076 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 578) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 579) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 22, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 22, 14, 14, 3, 4, 4, 4, 4, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 580) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 581) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@@H]1c1ccc(Cl)c(F)c1) `ZINC001632010076.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010076 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 34, 34, 34, 34, 34, 34, 34, 23, 23, 23, 23, 23, 23, 23, 13, 13, 3, 5, 5, 5, 5, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010076 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010076 Building ZINC001632010079 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010079 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/582 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 38, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 23, 23, 23, 15, 15, 3, 5, 5, 5, 5, 38, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/583 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 38, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 23, 23, 23, 15, 15, 3, 5, 5, 5, 5, 38, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/584 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/584' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 14, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 14, 14, 3, 5, 5, 5, 5, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/585 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/585' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 14, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 14, 14, 3, 5, 5, 5, 5, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010079 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 Building ZINC001632010079 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010079 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 582) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 38, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 23, 23, 23, 15, 15, 3, 5, 5, 5, 5, 38, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 583) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 38, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 23, 23, 23, 15, 15, 3, 5, 5, 5, 5, 38, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 584) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 14, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 14, 14, 3, 5, 5, 5, 5, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 585) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 14, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 14, 14, 3, 5, 5, 5, 5, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010079 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 Building ZINC001632010079 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010079 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 582) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 38, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 23, 23, 23, 15, 15, 3, 5, 5, 5, 5, 38, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 583) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 38, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 23, 23, 23, 15, 15, 3, 5, 5, 5, 5, 38, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 584) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 14, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 14, 14, 3, 5, 5, 5, 5, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 585) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 14, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 14, 14, 3, 5, 5, 5, 5, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010079 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 Building ZINC001632010079 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001632010079 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 582) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 38, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 23, 23, 23, 15, 15, 3, 5, 5, 5, 5, 38, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 583) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 23, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 38, 38, 38, 38, 38, 38, 38, 23, 23, 23, 23, 23, 23, 23, 15, 15, 3, 5, 5, 5, 5, 38, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 584) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 14, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 14, 14, 3, 5, 5, 5, 5, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 585) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2c[nH]c3cc(F)ccc32)[C@H]1c1ccc(Cl)c(F)c1) `ZINC001632010079.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001632010079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001632010079 none CN1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)[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.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', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 14, 25, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 37, 37, 37, 37, 37, 37, 37, 25, 25, 25, 25, 25, 25, 25, 14, 14, 3, 5, 5, 5, 5, 37, 37, 37] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632010079 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632010079 Building ZINC001632066950 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632066950 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/586 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/586' -> `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@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001632066950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632066950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001632066950 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 21, 34, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 3, 21, 21, 34, 34, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/587 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/587' -> `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@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001632066950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632066950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001632066950 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 20, 35, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 3, 20, 20, 35, 35, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632066950 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 Building ZINC001632066950 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632066950 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 586) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001632066950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632066950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001632066950 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 21, 34, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 3, 21, 21, 34, 34, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 587) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001632066950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632066950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001632066950 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 20, 35, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 2, 2, 2, 2, 2, 2, 3, 20, 20, 35, 35, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632066950 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066950 Building ZINC001632066951 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632066951 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/588 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/588' -> `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@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001632066951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632066951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001632066951 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 21, 35, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 3, 21, 21, 35, 35, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 206 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/589 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/589' -> `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@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001632066951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632066951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001632066951 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 21, 34, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 3, 21, 21, 34, 34, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632066951 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 Building ZINC001632066951 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632066951 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 588) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001632066951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632066951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001632066951 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 21, 35, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 3, 21, 21, 35, 35, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 206 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 589) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21) `ZINC001632066951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632066951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001632066951 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CN(C(=O)OC(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 21, 34, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 3, 21, 21, 34, 34, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632066951 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632066951 Building ZINC001632097972 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632097972 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/590 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccccc2Cl)CC1) `ZINC001632097972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632097972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632097972 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccccc2Cl)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', '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', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 8, 19, 19, 19, 19, 34, 34, 40, 40, 34, 40, 40, 34, 40, 40, 34, 40, 40, 40, 19, 19, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 40, 40, 34, 40, 40, 40, 40, 34, 40, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/591 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccccc2Cl)CC1) `ZINC001632097972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632097972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632097972 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccccc2Cl)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', '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', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 7, 20, 20, 20, 20, 33, 33, 37, 37, 33, 37, 37, 33, 36, 36, 33, 36, 36, 36, 20, 20, 6, 6, 6, 5, 5, 5, 5, 20, 20, 20, 20, 37, 37, 33, 37, 37, 36, 36, 33, 36, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632097972 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 Building ZINC001632097972 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632097972 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 590) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccccc2Cl)CC1) `ZINC001632097972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632097972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632097972 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccccc2Cl)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', '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', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 8, 19, 19, 19, 19, 34, 34, 40, 40, 34, 40, 40, 34, 40, 40, 34, 40, 40, 40, 19, 19, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 40, 40, 34, 40, 40, 40, 40, 34, 40, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 591) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccccc2Cl)CC1) `ZINC001632097972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632097972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632097972 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccccc2Cl)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', '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', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 7, 20, 20, 20, 20, 33, 33, 37, 37, 33, 37, 37, 33, 36, 36, 33, 36, 36, 36, 20, 20, 6, 6, 6, 5, 5, 5, 5, 20, 20, 20, 20, 37, 37, 33, 37, 37, 36, 36, 33, 36, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632097972 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097972 Building ZINC001632097973 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632097973 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/592 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccccc2Cl)CC1) `ZINC001632097973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632097973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632097973 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccccc2Cl)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', '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', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 8, 18, 18, 18, 18, 31, 31, 35, 35, 35, 35, 35, 31, 37, 37, 31, 37, 37, 37, 18, 18, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 35, 35, 35, 35, 35, 37, 37, 37, 37, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/593 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccccc2Cl)CC1) `ZINC001632097973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632097973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632097973 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccccc2Cl)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', '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', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 7, 23, 23, 23, 23, 35, 35, 42, 42, 42, 42, 42, 35, 40, 40, 35, 40, 40, 40, 23, 23, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 42, 42, 42, 42, 42, 40, 40, 40, 40, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632097973 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 Building ZINC001632097973 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632097973 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 592) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccccc2Cl)CC1) `ZINC001632097973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632097973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632097973 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccccc2Cl)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', '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', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 8, 18, 18, 18, 18, 31, 31, 35, 35, 35, 35, 35, 31, 37, 37, 31, 37, 37, 37, 18, 18, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 35, 35, 35, 35, 35, 37, 37, 37, 37, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 593) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccccc2Cl)CC1) `ZINC001632097973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632097973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632097973 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccccc2Cl)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', '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', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 7, 23, 23, 23, 23, 35, 35, 42, 42, 42, 42, 42, 35, 40, 40, 35, 40, 40, 40, 23, 23, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 42, 42, 42, 42, 42, 40, 40, 40, 40, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632097973 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632097973 Building ZINC001632102645 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632102645 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/594 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2CC[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001632102645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632102645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001632102645 none CC(C)(C)OC(=O)N1c2ccccc2CC[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 44, 47, 44, 44, 44, 44, 44, 44, 44, 44, 44, 29, 44, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 44, 44, 24, 24, 15, 15, 3, 2, 2, 2, 2] 50 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, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/595 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2CC[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001632102645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632102645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001632102645 none CC(C)(C)OC(=O)N1c2ccccc2CC[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 43, 47, 43, 43, 43, 43, 43, 43, 43, 43, 43, 31, 43, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 43, 43, 26, 26, 18, 18, 4, 3, 3, 3, 3] 50 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, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632102645 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 Building ZINC001632102645 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632102645 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 594) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1c2ccccc2CC[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001632102645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632102645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001632102645 none CC(C)(C)OC(=O)N1c2ccccc2CC[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 44, 47, 44, 44, 44, 44, 44, 44, 44, 44, 44, 29, 44, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 44, 44, 24, 24, 15, 15, 3, 2, 2, 2, 2] 50 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, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 595) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1c2ccccc2CC[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001632102645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632102645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001632102645 none CC(C)(C)OC(=O)N1c2ccccc2CC[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 43, 47, 43, 43, 43, 43, 43, 43, 43, 43, 43, 31, 43, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 43, 43, 26, 26, 18, 18, 4, 3, 3, 3, 3] 50 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, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632102645 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102645 Building ZINC001632102646 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632102646 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/596 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2CC[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001632102646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632102646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001632102646 none CC(C)(C)OC(=O)N1c2ccccc2CC[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 40, 49, 40, 40, 40, 40, 40, 40, 40, 40, 40, 29, 40, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 40, 40, 24, 24, 17, 17, 3, 3, 3, 3, 3] 50 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, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/597 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1c2ccccc2CC[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001632102646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632102646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001632102646 none CC(C)(C)OC(=O)N1c2ccccc2CC[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 38, 47, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 38, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 22, 22, 15, 15, 3, 2, 2, 2, 2] 50 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, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632102646 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 Building ZINC001632102646 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632102646 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 596) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1c2ccccc2CC[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001632102646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632102646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001632102646 none CC(C)(C)OC(=O)N1c2ccccc2CC[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 40, 49, 40, 40, 40, 40, 40, 40, 40, 40, 40, 29, 40, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 40, 40, 40, 40, 24, 24, 17, 17, 3, 3, 3, 3, 3] 50 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, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 597) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1c2ccccc2CC[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001632102646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632102646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001632102646 none CC(C)(C)OC(=O)N1c2ccccc2CC[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 38, 47, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 38, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 22, 22, 15, 15, 3, 2, 2, 2, 2] 50 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, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632102646 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632102646 Building ZINC001632122445 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632122445 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/598 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/598' -> `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)N1CCO[C@H](c2c(F)cccc2Cl)C1) `ZINC001632122445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632122445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001632122445 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2c(F)cccc2Cl)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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 6, 6, 12, 12, 12, 12, 12, 12, 33, 33, 33, 12, 33, 33, 33, 12, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 12, 12, 12, 12, 33, 19, 33, 12, 12] 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]) total number of confs: 126 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/599 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/599' -> `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)N1CCO[C@H](c2c(F)cccc2Cl)C1) `ZINC001632122445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632122445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001632122445 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2c(F)cccc2Cl)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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 9, 9, 4, 4, 1, 1, 1, 2, 5, 6, 12, 12, 12, 12, 12, 12, 30, 30, 30, 12, 30, 30, 30, 12, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 12, 12, 12, 12, 30, 16, 30, 12, 12] 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]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632122445 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 Building ZINC001632122445 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632122445 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 598) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2c(F)cccc2Cl)C1) `ZINC001632122445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632122445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001632122445 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2c(F)cccc2Cl)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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 6, 6, 12, 12, 12, 12, 12, 12, 33, 33, 33, 12, 33, 33, 33, 12, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 12, 12, 12, 12, 33, 19, 33, 12, 12] 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]) total number of confs: 126 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 599) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2c(F)cccc2Cl)C1) `ZINC001632122445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632122445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001632122445 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2c(F)cccc2Cl)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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 9, 9, 4, 4, 1, 1, 1, 2, 5, 6, 12, 12, 12, 12, 12, 12, 30, 30, 30, 12, 30, 30, 30, 12, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 12, 12, 12, 12, 30, 16, 30, 12, 12] 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]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632122445 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122445 Building ZINC001632122446 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632122446 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/600 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/600' -> `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)N1CCO[C@@H](c2c(F)cccc2Cl)C1) `ZINC001632122446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632122446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001632122446 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2c(F)cccc2Cl)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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 12, 12, 12, 12, 12, 12, 30, 30, 30, 12, 30, 30, 30, 12, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 12, 12, 12, 12, 30, 16, 30, 12, 12] 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]) total number of confs: 115 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/601 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/601' -> `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)N1CCO[C@@H](c2c(F)cccc2Cl)C1) `ZINC001632122446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632122446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001632122446 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2c(F)cccc2Cl)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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 5, 6, 12, 12, 12, 12, 12, 12, 34, 34, 34, 17, 34, 34, 34, 12, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 12, 12, 12, 12, 34, 21, 34, 12, 12] 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]) total number of confs: 119 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632122446 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 Building ZINC001632122446 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632122446 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 600) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2c(F)cccc2Cl)C1) `ZINC001632122446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632122446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001632122446 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2c(F)cccc2Cl)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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 12, 12, 12, 12, 12, 12, 30, 30, 30, 12, 30, 30, 30, 12, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 12, 12, 12, 12, 30, 16, 30, 12, 12] 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]) total number of confs: 115 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 601) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2c(F)cccc2Cl)C1) `ZINC001632122446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632122446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001632122446 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2c(F)cccc2Cl)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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 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, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 5, 6, 12, 12, 12, 12, 12, 12, 34, 34, 34, 17, 34, 34, 34, 12, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 12, 12, 12, 12, 34, 21, 34, 12, 12] 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]) total number of confs: 119 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632122446 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632122446 Building ZINC001632154364 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632154364 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/602 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001632154364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632154364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001632154364 none CC(C)(C)OC(=O)N[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 27, 13, 7, 13, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 13, 18, 18, 18, 18, 18, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 7, 7, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/603 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001632154364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632154364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001632154364 none CC(C)(C)OC(=O)N[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 27, 14, 8, 14, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 18, 18, 18, 18, 18, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 8, 8, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632154364 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 Building ZINC001632154364 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632154364 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 602) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001632154364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632154364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001632154364 none CC(C)(C)OC(=O)N[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 27, 13, 7, 13, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 13, 18, 18, 18, 18, 18, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 7, 7, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 603) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001632154364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632154364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001632154364 none CC(C)(C)OC(=O)N[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 27, 14, 8, 14, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 18, 18, 18, 18, 18, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 8, 8, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632154364 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154364 Building ZINC001632154365 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632154365 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/604 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001632154365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632154365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001632154365 none CC(C)(C)OC(=O)N[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 22, 28, 14, 8, 14, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 19, 19, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 22, 8, 8, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/605 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001632154365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632154365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001632154365 none CC(C)(C)OC(=O)N[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 26, 13, 7, 13, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 13, 17, 17, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 7, 7, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632154365 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 Building ZINC001632154365 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632154365 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 604) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001632154365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632154365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001632154365 none CC(C)(C)OC(=O)N[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 22, 28, 14, 8, 14, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 19, 19, 19, 19, 19, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 22, 8, 8, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 605) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001632154365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632154365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001632154365 none CC(C)(C)OC(=O)N[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 26, 13, 7, 13, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 13, 17, 17, 17, 17, 17, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 7, 7, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632154365 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632154365 Building ZINC001632176973 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632176973 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/606 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cccnc2cc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001632176973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632176973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001632176973 none O=C(NCc1cc2cccnc2cc1Br)[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', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 28, 28, 28, 28, 28, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/607 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cccnc2cc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001632176973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632176973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001632176973 none O=C(NCc1cc2cccnc2cc1Br)[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', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 28, 28, 28, 28, 28, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632176973 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 Building ZINC001632176973 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632176973 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 606) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NCc1cc2cccnc2cc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001632176973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632176973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001632176973 none O=C(NCc1cc2cccnc2cc1Br)[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', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 28, 28, 28, 28, 28, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 607) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NCc1cc2cccnc2cc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001632176973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632176973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001632176973 none O=C(NCc1cc2cccnc2cc1Br)[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', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 28, 28, 28, 28, 28, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632176973 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632176973 Building ZINC001632278907 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632278907 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/608 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2ccccc2n1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632278907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632278907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001632278907 none Cc1nc2ccccc2n1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [31, 31, 31, 31, 31, 31, 31, 31, 31, 26, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 26, 26, 13, 13, 13, 13, 13, 13, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/609 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2ccccc2n1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632278907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632278907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001632278907 none Cc1nc2ccccc2n1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 19, 19, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 84 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632278907 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 Building ZINC001632278907 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632278907 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 608) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nc2ccccc2n1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632278907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632278907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001632278907 none Cc1nc2ccccc2n1C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [31, 31, 31, 31, 31, 31, 31, 31, 31, 26, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 26, 26, 13, 13, 13, 13, 13, 13, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 609) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nc2ccccc2n1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632278907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632278907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001632278907 none Cc1nc2ccccc2n1C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 19, 19, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 84 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632278907 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278907 Building ZINC001632278915 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632278915 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/610 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2ccccc2n1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632278915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632278915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001632278915 none Cc1nc2ccccc2n1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 14, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 34, 34, 34, 34, 34, 34, 34, 26, 26, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/611 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2ccccc2n1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632278915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632278915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001632278915 none Cc1nc2ccccc2n1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [31, 31, 31, 31, 31, 31, 31, 31, 31, 26, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 26, 26, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 110 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632278915 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 Building ZINC001632278915 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632278915 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 610) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nc2ccccc2n1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632278915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632278915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001632278915 none Cc1nc2ccccc2n1C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [34, 34, 34, 34, 34, 34, 34, 34, 34, 26, 14, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 34, 34, 34, 34, 34, 34, 34, 26, 26, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 611) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nc2ccccc2n1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632278915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632278915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001632278915 none Cc1nc2ccccc2n1C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 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, 7, 7, 7, 9, 6, 8, 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: [31, 31, 31, 31, 31, 31, 31, 31, 31, 26, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 26, 26, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 110 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632278915 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632278915 Building ZINC001632330811 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632330811 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/612 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccc(Cl)cc2)CC1) `ZINC001632330811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632330811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632330811 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 6, 17, 17, 17, 17, 33, 33, 38, 38, 33, 38, 38, 33, 38, 38, 38, 38, 38, 38, 17, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 38, 38, 38, 38, 38, 38, 38, 38, 38, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/613 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccc(Cl)cc2)CC1) `ZINC001632330811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632330811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632330811 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 3, 6, 18, 18, 18, 18, 28, 28, 35, 35, 28, 35, 35, 28, 32, 32, 28, 32, 32, 32, 18, 18, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 35, 35, 35, 35, 35, 32, 32, 32, 32, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632330811 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 Building ZINC001632330811 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632330811 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 612) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccc(Cl)cc2)CC1) `ZINC001632330811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632330811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632330811 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 6, 17, 17, 17, 17, 33, 33, 38, 38, 33, 38, 38, 33, 38, 38, 38, 38, 38, 38, 17, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 38, 38, 38, 38, 38, 38, 38, 38, 38, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 613) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccc(Cl)cc2)CC1) `ZINC001632330811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632330811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632330811 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](c2ccccc2)c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 3, 6, 18, 18, 18, 18, 28, 28, 35, 35, 28, 35, 35, 28, 32, 32, 28, 32, 32, 32, 18, 18, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 35, 35, 35, 35, 35, 32, 32, 32, 32, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632330811 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330811 Building ZINC001632330812 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632330812 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/614 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccc(Cl)cc2)CC1) `ZINC001632330812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632330812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632330812 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 7, 17, 17, 17, 17, 32, 32, 37, 37, 37, 37, 37, 32, 38, 38, 32, 32, 38, 38, 17, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 37, 37, 37, 37, 37, 38, 38, 38, 38, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/615 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccc(Cl)cc2)CC1) `ZINC001632330812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632330812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632330812 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 3, 6, 18, 18, 18, 18, 28, 28, 32, 32, 32, 32, 32, 28, 35, 35, 35, 35, 35, 35, 18, 18, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 32, 32, 32, 32, 32, 35, 35, 35, 35, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632330812 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 Building ZINC001632330812 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632330812 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 614) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccc(Cl)cc2)CC1) `ZINC001632330812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632330812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632330812 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 7, 17, 17, 17, 17, 32, 32, 37, 37, 37, 37, 37, 32, 38, 38, 32, 32, 38, 38, 17, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 37, 37, 37, 37, 37, 38, 38, 38, 38, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 615) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccc(Cl)cc2)CC1) `ZINC001632330812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632330812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001632330812 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](c2ccccc2)c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 3, 6, 18, 18, 18, 18, 28, 28, 32, 32, 32, 32, 32, 28, 35, 35, 35, 35, 35, 35, 18, 18, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 32, 32, 32, 32, 32, 35, 35, 35, 35, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632330812 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632330812 Building ZINC001632367984 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632367984 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/616 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)c(Cl)c3)CC2)cc1Cl) `ZINC001632367984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632367984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001632367984 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)c(Cl)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 8, 8, 8, 8, 8, 28, 28, 20, 28, 28, 28, 28, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 8, 8, 8, 8, 28, 28, 28, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/617 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)c(Cl)c3)CC2)cc1Cl) `ZINC001632367984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632367984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001632367984 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)c(Cl)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 27, 27, 19, 27, 27, 27, 27, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 8, 8, 8, 8, 27, 27, 27, 8, 8, 8, 8, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632367984 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 Building ZINC001632367984 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632367984 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 616) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)c(Cl)c3)CC2)cc1Cl) `ZINC001632367984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632367984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001632367984 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)c(Cl)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 8, 8, 8, 8, 8, 28, 28, 20, 28, 28, 28, 28, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 8, 8, 8, 8, 28, 28, 28, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 617) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)c(Cl)c3)CC2)cc1Cl) `ZINC001632367984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632367984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001632367984 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)c(Cl)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 27, 27, 19, 27, 27, 27, 27, 8, 8, 2, 2, 2, 4, 4, 4, 2, 2, 8, 8, 8, 8, 27, 27, 27, 8, 8, 8, 8, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632367984 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632367984 Building ZINC001632378401 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632378401 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/618 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)cc3Cl)CC2)cc1Cl) `ZINC001632378401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632378401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001632378401 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)cc3Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 1, 1, 1, 2, 5, 8, 10, 10, 10, 10, 24, 24, 10, 13, 24, 24, 24, 10, 10, 6, 6, 6, 8, 8, 8, 6, 6, 10, 10, 10, 10, 24, 24, 24, 10, 10, 10, 10, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/619 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)cc3Cl)CC2)cc1Cl) `ZINC001632378401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632378401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001632378401 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)cc3Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 1, 1, 1, 2, 3, 7, 9, 9, 9, 9, 23, 23, 9, 11, 23, 23, 23, 9, 9, 6, 6, 6, 8, 8, 8, 6, 6, 9, 9, 9, 9, 23, 23, 23, 9, 9, 9, 9, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632378401 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 Building ZINC001632378401 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632378401 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 618) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)cc3Cl)CC2)cc1Cl) `ZINC001632378401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632378401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001632378401 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)cc3Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 1, 1, 1, 2, 5, 8, 10, 10, 10, 10, 24, 24, 10, 13, 24, 24, 24, 10, 10, 6, 6, 6, 8, 8, 8, 6, 6, 10, 10, 10, 10, 24, 24, 24, 10, 10, 10, 10, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 619) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)cc3Cl)CC2)cc1Cl) `ZINC001632378401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632378401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001632378401 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Cl)cc3Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 2, 6, 6, 1, 1, 1, 2, 3, 7, 9, 9, 9, 9, 23, 23, 9, 11, 23, 23, 23, 9, 9, 6, 6, 6, 8, 8, 8, 6, 6, 9, 9, 9, 9, 23, 23, 23, 9, 9, 9, 9, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632378401 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632378401 Building ZINC001632669658 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632669658 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/620 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nc2ccc(C(F)(F)F)cc2[nH]1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632669658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632669658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001632669658 none CN(Cc1nc2ccc(C(F)(F)F)cc2[nH]1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 6, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 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, 7, 9, 6, 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: [8, 4, 8, 22, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 22, 22, 33, 33, 33, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/621 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nc2ccc(C(F)(F)F)cc2[nH]1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632669658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632669658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001632669658 none CN(Cc1nc2ccc(C(F)(F)F)cc2[nH]1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 6, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 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, 7, 9, 6, 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: [7, 4, 7, 21, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 21, 21, 32, 32, 32, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632669658 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 Building ZINC001632669658 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632669658 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 620) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nc2ccc(C(F)(F)F)cc2[nH]1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632669658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632669658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001632669658 none CN(Cc1nc2ccc(C(F)(F)F)cc2[nH]1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 6, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 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, 7, 9, 6, 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: [8, 4, 8, 22, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 22, 22, 33, 33, 33, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 621) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nc2ccc(C(F)(F)F)cc2[nH]1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001632669658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632669658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001632669658 none CN(Cc1nc2ccc(C(F)(F)F)cc2[nH]1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 6, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 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, 7, 9, 6, 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: [7, 4, 7, 21, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 21, 21, 32, 32, 32, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632669658 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632669658 Building ZINC001632770210 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632770210 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/622 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(NC(C)C)c1) `ZINC001632770210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632770210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001632770210 none CCOC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(NC(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 5, 5, 5, 1, 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, 3, 7, 5, 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] 0 hydrogens 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, 12, 12, 5, 12, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 12, 17, 17, 5, 28, 28, 28, 28, 28, 5, 5, 2, 5, 5, 12, 17, 17, 17, 17, 17, 17, 17, 5] 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/623 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(NC(C)C)c1) `ZINC001632770210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632770210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001632770210 none CCOC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(NC(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 5, 5, 5, 1, 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, 3, 7, 5, 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] 0 hydrogens 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, 12, 12, 5, 12, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 5, 5, 12, 17, 17, 5, 28, 28, 28, 28, 28, 5, 5, 2, 6, 6, 12, 17, 17, 17, 17, 17, 17, 17, 5] 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: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632770210 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 Building ZINC001632770210 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632770210 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 622) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(NC(C)C)c1) `ZINC001632770210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632770210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001632770210 none CCOC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(NC(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 5, 5, 5, 1, 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, 3, 7, 5, 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] 0 hydrogens 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, 12, 12, 5, 12, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 12, 17, 17, 5, 28, 28, 28, 28, 28, 5, 5, 2, 5, 5, 12, 17, 17, 17, 17, 17, 17, 17, 5] 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 623) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(NC(C)C)c1) `ZINC001632770210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632770210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001632770210 none CCOC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(NC(C)C)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 5, 5, 5, 1, 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, 3, 7, 5, 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] 0 hydrogens 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, 12, 12, 5, 12, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 5, 5, 12, 17, 17, 5, 28, 28, 28, 28, 28, 5, 5, 2, 6, 6, 12, 17, 17, 17, 17, 17, 17, 17, 5] 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: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632770210 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632770210 Building ZINC001632952995 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632952995 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/624 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@H]2C(C)C)cn1) `ZINC001632952995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632952995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952995 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 21, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 34, 34, 5, 5, 12, 12, 12, 12, 12, 5, 3, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 34, 34, 34, 34, 34, 34, 34, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 147 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/625 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@H]2C(C)C)cn1) `ZINC001632952995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632952995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952995 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 12, 12, 22, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 34, 34, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 34, 34, 34, 34, 34, 34, 34, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632952995 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 Building ZINC001632952995 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632952995 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 624) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@H]2C(C)C)cn1) `ZINC001632952995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632952995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952995 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 21, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 34, 34, 5, 5, 12, 12, 12, 12, 12, 5, 3, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 34, 34, 34, 34, 34, 34, 34, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 147 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 625) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@H]2C(C)C)cn1) `ZINC001632952995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632952995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952995 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 12, 12, 22, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 34, 34, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 34, 34, 34, 34, 34, 34, 34, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632952995 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952995 Building ZINC001632952996 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632952996 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/626 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@@H]2C(C)C)cn1) `ZINC001632952996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632952996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952996 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 14, 14, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 32, 32, 4, 4, 8, 8, 8, 8, 8, 4, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 32, 32, 32, 32, 32, 32, 32, 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, 56, 57, 58, 59, 60, 61]) total number of confs: 133 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/627 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@@H]2C(C)C)cn1) `ZINC001632952996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632952996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952996 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 13, 13, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 30, 30, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 30, 30, 30, 30, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 127 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632952996 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 Building ZINC001632952996 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632952996 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 626) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@@H]2C(C)C)cn1) `ZINC001632952996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632952996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952996 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 14, 14, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 32, 32, 4, 4, 8, 8, 8, 8, 8, 4, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 32, 32, 32, 32, 32, 32, 32, 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, 56, 57, 58, 59, 60, 61]) total number of confs: 133 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 627) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@@H]2C(C)C)cn1) `ZINC001632952996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632952996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952996 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 13, 13, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 30, 30, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 30, 30, 30, 30, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 127 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632952996 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952996 Building ZINC001632952997 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632952997 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/628 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@H]2C(C)C)cn1) `ZINC001632952997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632952997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952997 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 13, 13, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 33, 33, 5, 5, 11, 11, 11, 11, 11, 5, 3, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 33, 33, 33, 33, 33, 33, 33, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/629 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@H]2C(C)C)cn1) `ZINC001632952997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632952997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952997 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 10, 10, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 30, 30, 6, 6, 14, 14, 14, 14, 14, 6, 2, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 30, 30, 30, 30, 30, 30, 30, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632952997 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 Building ZINC001632952997 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632952997 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 628) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@H]2C(C)C)cn1) `ZINC001632952997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632952997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952997 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 13, 13, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 33, 33, 5, 5, 11, 11, 11, 11, 11, 5, 3, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 33, 33, 33, 33, 33, 33, 33, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 629) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@H]2C(C)C)cn1) `ZINC001632952997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632952997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952997 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@H](C)CC[C@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 10, 10, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 30, 30, 6, 6, 14, 14, 14, 14, 14, 6, 2, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 30, 30, 30, 30, 30, 30, 30, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632952997 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952997 Building ZINC001632952998 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632952998 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/630 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@@H]2C(C)C)cn1) `ZINC001632952998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632952998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952998 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 22, 22, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 35, 35, 3, 3, 6, 6, 6, 6, 6, 3, 3, 5, 5, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 35, 35, 35, 35, 35, 35, 35, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/631 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@@H]2C(C)C)cn1) `ZINC001632952998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632952998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952998 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 21, 21, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 35, 35, 5, 5, 9, 9, 9, 9, 9, 5, 2, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 35, 35, 35, 35, 35, 35, 35, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632952998 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 Building ZINC001632952998 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632952998 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 630) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@@H]2C(C)C)cn1) `ZINC001632952998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632952998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952998 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 22, 22, 27, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 35, 35, 3, 3, 6, 6, 6, 6, 6, 3, 3, 5, 5, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 35, 35, 35, 35, 35, 35, 35, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 631) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@@H]2C(C)C)cn1) `ZINC001632952998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632952998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001632952998 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)O[C@@H]2C[C@@H](C)CC[C@@H]2C(C)C)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 21, 21, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 35, 35, 5, 5, 9, 9, 9, 9, 9, 5, 2, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 35, 35, 35, 35, 35, 35, 35, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001632952998 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001632952998 Building ZINC001633026089 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633026089 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/632 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001633026089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633026089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633026089 none CC(C)(C)OC(=O)NCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 33, 45, 17, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 33, 17, 17, 2, 8, 8, 2, 5, 5, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/633 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001633026089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633026089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633026089 none CC(C)(C)OC(=O)NCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 33, 44, 19, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 33, 19, 19, 8, 8, 8, 2, 6, 6, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633026089 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 Building ZINC001633026089 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633026089 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 632) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001633026089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633026089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633026089 none CC(C)(C)OC(=O)NCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 33, 45, 17, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 33, 17, 17, 2, 8, 8, 2, 5, 5, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 633) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001633026089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633026089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633026089 none CC(C)(C)OC(=O)NCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 33, 44, 19, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 8, 44, 44, 44, 44, 44, 44, 44, 44, 44, 33, 19, 19, 8, 8, 8, 2, 6, 6, 8] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633026089 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633026089 Building ZINC001633030500 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633030500 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/634 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC23CCC3)CC1) `ZINC001633030500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633030500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633030500 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC23CCC3)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 12, 12, 12, 12, 25, 25, 25, 44, 44, 50, 50, 50, 50, 25, 25, 25, 25, 25, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 140 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/635 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC23CCC3)CC1) `ZINC001633030500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633030500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633030500 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC23CCC3)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 10, 10, 10, 10, 27, 27, 27, 43, 43, 50, 50, 50, 50, 27, 27, 27, 27, 27, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 137 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633030500 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 Building ZINC001633030500 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633030500 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 634) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC23CCC3)CC1) `ZINC001633030500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633030500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633030500 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC23CCC3)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 12, 12, 12, 12, 25, 25, 25, 44, 44, 50, 50, 50, 50, 25, 25, 25, 25, 25, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 140 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 635) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC23CCC3)CC1) `ZINC001633030500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633030500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633030500 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC23CCC3)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 10, 10, 10, 10, 27, 27, 27, 43, 43, 50, 50, 50, 50, 27, 27, 27, 27, 27, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 137 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633030500 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030500 Building ZINC001633030503 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633030503 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/636 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC23CCC3)CC1) `ZINC001633030503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633030503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633030503 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC23CCC3)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 10, 10, 10, 10, 26, 26, 26, 44, 44, 50, 50, 50, 50, 26, 26, 26, 26, 26, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 146 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/637 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC23CCC3)CC1) `ZINC001633030503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633030503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633030503 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC23CCC3)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 12, 12, 12, 12, 25, 25, 25, 43, 43, 50, 50, 50, 50, 25, 25, 25, 25, 25, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633030503 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 Building ZINC001633030503 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633030503 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 636) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC23CCC3)CC1) `ZINC001633030503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633030503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633030503 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC23CCC3)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 10, 10, 10, 10, 26, 26, 26, 44, 44, 50, 50, 50, 50, 26, 26, 26, 26, 26, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 146 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 637) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC23CCC3)CC1) `ZINC001633030503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633030503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633030503 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC23CCC3)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 12, 12, 12, 12, 25, 25, 25, 43, 43, 50, 50, 50, 50, 25, 25, 25, 25, 25, 12, 12, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633030503 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633030503 Building ZINC001633032423 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633032423 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/638 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC([C@@H]3N(C(=O)OC(C)(C)C)CC34CCC4)CC2)cc1) `ZINC001633032423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633032423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633032423 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC([C@@H]3N(C(=O)OC(C)(C)C)CC34CCC4)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 9, 9, 9, 9, 20, 20, 20, 40, 40, 50, 50, 50, 50, 20, 20, 20, 20, 20, 9, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 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, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/639 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC([C@@H]3N(C(=O)OC(C)(C)C)CC34CCC4)CC2)cc1) `ZINC001633032423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633032423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633032423 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC([C@@H]3N(C(=O)OC(C)(C)C)CC34CCC4)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 8, 8, 8, 8, 22, 22, 22, 40, 40, 50, 50, 50, 50, 22, 22, 22, 22, 22, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 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, 60, 61, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633032423 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 Building ZINC001633032423 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633032423 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 638) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC([C@@H]3N(C(=O)OC(C)(C)C)CC34CCC4)CC2)cc1) `ZINC001633032423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633032423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633032423 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC([C@@H]3N(C(=O)OC(C)(C)C)CC34CCC4)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 9, 9, 9, 9, 20, 20, 20, 40, 40, 50, 50, 50, 50, 20, 20, 20, 20, 20, 9, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 9, 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, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 639) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC([C@@H]3N(C(=O)OC(C)(C)C)CC34CCC4)CC2)cc1) `ZINC001633032423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633032423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633032423 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC([C@@H]3N(C(=O)OC(C)(C)C)CC34CCC4)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 8, 8, 8, 8, 22, 22, 22, 40, 40, 50, 50, 50, 50, 22, 22, 22, 22, 22, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 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, 60, 61, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633032423 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032423 Building ZINC001633032424 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633032424 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/640 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC([C@H]3N(C(=O)OC(C)(C)C)CC34CCC4)CC2)cc1) `ZINC001633032424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633032424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633032424 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC([C@H]3N(C(=O)OC(C)(C)C)CC34CCC4)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 9, 9, 9, 9, 23, 23, 23, 41, 41, 50, 50, 50, 50, 23, 23, 23, 23, 23, 9, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 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, 60, 61, 62, 63, 64]) total number of confs: 147 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/641 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC([C@H]3N(C(=O)OC(C)(C)C)CC34CCC4)CC2)cc1) `ZINC001633032424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633032424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633032424 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC([C@H]3N(C(=O)OC(C)(C)C)CC34CCC4)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 10, 10, 10, 10, 19, 19, 19, 39, 39, 50, 50, 50, 50, 19, 19, 19, 19, 19, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 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, 60, 61, 62, 63, 64]) total number of confs: 144 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633032424 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 Building ZINC001633032424 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633032424 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 640) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC([C@H]3N(C(=O)OC(C)(C)C)CC34CCC4)CC2)cc1) `ZINC001633032424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633032424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633032424 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC([C@H]3N(C(=O)OC(C)(C)C)CC34CCC4)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 9, 9, 9, 9, 23, 23, 23, 41, 41, 50, 50, 50, 50, 23, 23, 23, 23, 23, 9, 9, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 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, 60, 61, 62, 63, 64]) total number of confs: 147 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 641) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC([C@H]3N(C(=O)OC(C)(C)C)CC34CCC4)CC2)cc1) `ZINC001633032424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633032424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001633032424 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC([C@H]3N(C(=O)OC(C)(C)C)CC34CCC4)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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 10, 10, 10, 10, 19, 19, 19, 39, 39, 50, 50, 50, 50, 19, 19, 19, 19, 19, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 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, 60, 61, 62, 63, 64]) total number of confs: 144 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633032424 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633032424 Building ZINC001633390147 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633390147 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/642 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(NC(=O)OC(C)(C)C)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001633390147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633390147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001633390147 none CCC1(NC(=O)OC(C)(C)C)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [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] 0 hydrogens 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, 15, 15, 15, 19, 36, 36, 50, 50, 50, 50, 15, 15, 8, 1, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 15, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 2, 15, 15, 15, 15] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/643 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(NC(=O)OC(C)(C)C)CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001633390147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633390147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001633390147 none CCC1(NC(=O)OC(C)(C)C)CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 16, 16, 21, 38, 38, 50, 50, 50, 50, 16, 16, 8, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 16, 16, 16, 16] 50 rigid atoms, others: [48, 49, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633390147 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 Building ZINC001633390147 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633390147 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 642) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC1(NC(=O)OC(C)(C)C)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001633390147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633390147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001633390147 none CCC1(NC(=O)OC(C)(C)C)CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [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] 0 hydrogens 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, 15, 15, 15, 19, 36, 36, 50, 50, 50, 50, 15, 15, 8, 1, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 15, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 2, 15, 15, 15, 15] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 643) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC1(NC(=O)OC(C)(C)C)CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001633390147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633390147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001633390147 none CCC1(NC(=O)OC(C)(C)C)CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 16, 16, 21, 38, 38, 50, 50, 50, 50, 16, 16, 8, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 16, 16, 16, 16] 50 rigid atoms, others: [48, 49, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633390147 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633390147 Building ZINC001633465233 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633465233 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/644 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/644' -> `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])c1c[nH]c2cc(F)ccc21)C1CCCCC1) `ZINC001633465233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633465233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001633465233 none CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 26, 29, 14, 6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 33, 33, 26, 14, 14, 3, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/645 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/645' -> `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])c1c[nH]c2cc(F)ccc21)C1CCCCC1) `ZINC001633465233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633465233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001633465233 none CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 32, 27, 32, 13, 5, 3, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 13, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 27, 13, 13, 3, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633465233 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 Building ZINC001633465233 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633465233 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 644) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCC1) `ZINC001633465233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633465233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001633465233 none CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 26, 29, 14, 6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 33, 33, 26, 14, 14, 3, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 645) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCC1) `ZINC001633465233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633465233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001633465233 none CC(C)(C)OC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 32, 27, 32, 13, 5, 3, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 13, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 27, 13, 13, 3, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633465233 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465233 Building ZINC001633465234 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633465234 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/646 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/646' -> `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])c1c[nH]c2cc(F)ccc21)C1CCCCC1) `ZINC001633465234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633465234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001633465234 none CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 5, 3, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 12, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 12, 12, 3, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/647 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/647' -> `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])c1c[nH]c2cc(F)ccc21)C1CCCCC1) `ZINC001633465234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633465234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001633465234 none CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 26, 14, 6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 24, 14, 14, 3, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633465234 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 Building ZINC001633465234 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633465234 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 646) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCC1) `ZINC001633465234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633465234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001633465234 none CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 5, 3, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 12, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 12, 12, 3, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 647) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCC1) `ZINC001633465234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633465234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001633465234 none CC(C)(C)OC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 26, 14, 6, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 24, 14, 14, 3, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633465234 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633465234 Building ZINC001633606414 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633606414 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/648 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC(F)(F)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001633606414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633606414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001633606414 none O=C(NCC(F)(F)c1ccc(Br)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', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 16, 16, 31, 31, 31, 31, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/649 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC(F)(F)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001633606414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633606414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001633606414 none O=C(NCC(F)(F)c1ccc(Br)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', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 17, 17, 32, 32, 32, 32, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633606414 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 Building ZINC001633606414 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633606414 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 648) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(NCC(F)(F)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001633606414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633606414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001633606414 none O=C(NCC(F)(F)c1ccc(Br)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', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 16, 16, 31, 31, 31, 31, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 649) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(NCC(F)(F)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001633606414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633606414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001633606414 none O=C(NCC(F)(F)c1ccc(Br)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', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 17, 17, 32, 32, 32, 32, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633606414 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633606414 Building ZINC001633692547 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633692547 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/650 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633692547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633692547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001633692547 none O=C(N1CC[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', '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'] dock atom type numbers: [11, 1, 8, 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] 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] 0 hydrogens 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, 17, 17, 17, 17, 17, 29, 29, 17, 19, 29, 29, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 17, 17, 29, 29, 29, 29, 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/651 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633692547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633692547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001633692547 none O=C(N1CC[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', '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'] dock atom type numbers: [11, 1, 8, 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] 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] 0 hydrogens 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, 20, 20, 20, 20, 20, 31, 31, 31, 31, 31, 31, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 20, 20, 31, 31, 31, 31, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633692547 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 Building ZINC001633692547 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633692547 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 650) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CC[C@@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633692547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633692547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001633692547 none O=C(N1CC[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', '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'] dock atom type numbers: [11, 1, 8, 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] 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] 0 hydrogens 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, 17, 17, 17, 17, 17, 29, 29, 17, 19, 29, 29, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 17, 17, 29, 29, 29, 29, 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 651) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CC[C@@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633692547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633692547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001633692547 none O=C(N1CC[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', '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'] dock atom type numbers: [11, 1, 8, 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] 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] 0 hydrogens 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, 20, 20, 20, 20, 20, 31, 31, 31, 31, 31, 31, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 20, 20, 31, 31, 31, 31, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633692547 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692547 Building ZINC001633692548 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633692548 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/652 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633692548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633692548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001633692548 none O=C(N1CC[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', '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'] dock atom type numbers: [11, 1, 8, 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] 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] 0 hydrogens 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, 19, 19, 19, 19, 19, 31, 31, 30, 31, 31, 31, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 31, 31, 31, 31, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/653 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633692548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633692548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001633692548 none O=C(N1CC[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', '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'] dock atom type numbers: [11, 1, 8, 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] 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] 0 hydrogens 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, 17, 17, 17, 17, 17, 29, 29, 17, 21, 29, 29, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 17, 17, 29, 29, 29, 29, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633692548 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 Building ZINC001633692548 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633692548 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 652) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CC[C@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633692548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633692548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001633692548 none O=C(N1CC[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', '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'] dock atom type numbers: [11, 1, 8, 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] 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] 0 hydrogens 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, 19, 19, 19, 19, 19, 31, 31, 30, 31, 31, 31, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 31, 31, 31, 31, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 653) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CC[C@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633692548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633692548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001633692548 none O=C(N1CC[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', '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'] dock atom type numbers: [11, 1, 8, 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] 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] 0 hydrogens 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, 17, 17, 17, 17, 17, 29, 29, 17, 21, 29, 29, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 17, 17, 29, 29, 29, 29, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633692548 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633692548 Building ZINC001633693965 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633693965 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/654 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cn2cc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)nc12) `ZINC001633693965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633693965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633693965 none Cc1cc(Br)cn2cc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', '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', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 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: [48, 48, 48, 48, 48, 48, 48, 48, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 3, 3, 1, 3] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/655 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cn2cc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)nc12) `ZINC001633693965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633693965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633693965 none Cc1cc(Br)cn2cc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', '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', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 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: [48, 48, 48, 48, 48, 48, 48, 48, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 3, 3, 1, 3] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633693965 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 Building ZINC001633693965 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633693965 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 654) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc(Br)cn2cc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)nc12) `ZINC001633693965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633693965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633693965 none Cc1cc(Br)cn2cc(CNC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', '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', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 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: [48, 48, 48, 48, 48, 48, 48, 48, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 3, 3, 1, 3] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 655) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc(Br)cn2cc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)nc12) `ZINC001633693965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633693965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633693965 none Cc1cc(Br)cn2cc(CNC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)nc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', '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', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 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: [48, 48, 48, 48, 48, 48, 48, 48, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 3, 3, 1, 3] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633693965 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633693965 Building ZINC001633767496 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633767496 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/656 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)c(Cl)c1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001633767496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633767496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633767496 none O=C(Nc1ccc(F)c(Cl)c1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 9, 31, 31, 31, 7, 7, 7, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/657 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)c(Cl)c1)C1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001633767496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633767496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633767496 none O=C(Nc1ccc(F)c(Cl)c1)C1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 9, 31, 31, 31, 7, 7, 7, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633767496 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 Building ZINC001633767496 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633767496 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 656) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccc(F)c(Cl)c1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001633767496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633767496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633767496 none O=C(Nc1ccc(F)c(Cl)c1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 9, 31, 31, 31, 7, 7, 7, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 657) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccc(F)c(Cl)c1)C1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001633767496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633767496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633767496 none O=C(Nc1ccc(F)c(Cl)c1)C1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 9, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 9, 31, 31, 31, 7, 7, 7, 7, 7, 3, 3, 3, 3, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633767496 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633767496 Building ZINC001633780324 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633780324 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/658 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)c2ccc(Br)cc2)cc1) `ZINC001633780324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633780324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001633780324 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)c2ccc(Br)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 14, 14, 20, 20, 20, 20, 20, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/659 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)c2ccc(Br)cc2)cc1) `ZINC001633780324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633780324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001633780324 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)c2ccc(Br)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 14, 14, 20, 20, 20, 20, 20, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633780324 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 Building ZINC001633780324 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633780324 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 658) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)c2ccc(Br)cc2)cc1) `ZINC001633780324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633780324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001633780324 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)c2ccc(Br)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 14, 14, 20, 20, 20, 20, 20, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 659) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)c2ccc(Br)cc2)cc1) `ZINC001633780324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633780324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001633780324 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(CNC(=O)c2ccc(Br)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 14, 14, 20, 20, 20, 20, 20, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633780324 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633780324 Building ZINC001633784066 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633784066 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/660 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/660' -> `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)c2ccncc2)cc1) `ZINC001633784066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633784066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001633784066 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 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, 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, 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, 25, 25, 25, 25, 25, 9, 9, 6, 6, 6, 3, 4, 4, 4, 4, 9, 9, 21, 25, 25, 25, 25, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/661 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/661' -> `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)c2ccncc2)cc1) `ZINC001633784066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633784066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001633784066 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 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, 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, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 10, 10, 6, 7, 25, 25, 25, 32, 32, 25, 32, 32, 10, 10, 6, 6, 6, 3, 5, 5, 5, 5, 10, 10, 25, 32, 32, 32, 32, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633784066 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 Building ZINC001633784066 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633784066 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 660) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001633784066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633784066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001633784066 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 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, 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, 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, 25, 25, 25, 25, 25, 9, 9, 6, 6, 6, 3, 4, 4, 4, 4, 9, 9, 21, 25, 25, 25, 25, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 661) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001633784066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633784066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001633784066 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 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, 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, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 10, 10, 6, 7, 25, 25, 25, 32, 32, 25, 32, 32, 10, 10, 6, 6, 6, 3, 5, 5, 5, 5, 10, 10, 25, 32, 32, 32, 32, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633784066 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784066 Building ZINC001633784067 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633784067 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/662 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/662' -> `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)c2ccncc2)cc1) `ZINC001633784067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633784067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001633784067 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 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, 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: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 11, 11, 10, 10, 23, 23, 23, 30, 30, 30, 30, 30, 11, 11, 7, 7, 7, 4, 6, 6, 6, 6, 11, 11, 23, 30, 30, 30, 30, 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/663 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/663' -> `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)c2ccncc2)cc1) `ZINC001633784067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633784067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001633784067 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 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, 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, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 9, 9, 9, 9, 20, 20, 20, 25, 25, 20, 25, 25, 9, 9, 6, 6, 6, 3, 4, 4, 4, 4, 9, 9, 20, 25, 25, 25, 25, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633784067 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 Building ZINC001633784067 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633784067 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 662) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001633784067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633784067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001633784067 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 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, 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: [7, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 11, 11, 10, 10, 23, 23, 23, 30, 30, 30, 30, 30, 11, 11, 7, 7, 7, 4, 6, 6, 6, 6, 11, 11, 23, 30, 30, 30, 30, 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 663) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)cc1) `ZINC001633784067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633784067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001633784067 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(NC(=O)c2ccncc2)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 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, 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, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 9, 9, 9, 9, 20, 20, 20, 25, 25, 20, 25, 25, 9, 9, 6, 6, 6, 3, 4, 4, 4, 4, 9, 9, 20, 25, 25, 25, 25, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633784067 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633784067 Building ZINC001633787218 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633787218 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/664 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)([C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001633787218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633787218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001633787218 none CC(C)([C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 6, 6, 6, 6, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/665 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)([C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001633787218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633787218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001633787218 none CC(C)([C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 5, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 13, 13, 13, 13, 13, 5, 7, 7, 7, 7, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633787218 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 Building ZINC001633787218 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633787218 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 664) grep: /scratch/xiaobo/369383/xbb-8058088.28/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@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001633787218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633787218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001633787218 none CC(C)([C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 6, 6, 6, 6, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 665) grep: /scratch/xiaobo/369383/xbb-8058088.28/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@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001633787218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633787218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001633787218 none CC(C)([C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 5, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 13, 13, 13, 13, 13, 5, 7, 7, 7, 7, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633787218 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787218 Building ZINC001633787222 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633787222 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/666 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)([C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001633787222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633787222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001633787222 none CC(C)([C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 5, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 13, 13, 13, 13, 13, 5, 7, 7, 7, 7, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/667 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)([C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001633787222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633787222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001633787222 none CC(C)([C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 6, 6, 6, 6, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633787222 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 Building ZINC001633787222 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633787222 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 666) grep: /scratch/xiaobo/369383/xbb-8058088.28/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@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001633787222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633787222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001633787222 none CC(C)([C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 5, 7, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 15, 15, 15, 15, 13, 13, 13, 13, 13, 13, 5, 7, 7, 7, 7, 13, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 667) grep: /scratch/xiaobo/369383/xbb-8058088.28/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@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001633787222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633787222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001633787222 none CC(C)([C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 4, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 6, 6, 6, 6, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 67 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633787222 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633787222 Building ZINC001633867857 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633867857 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/668 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1c(F)cc(F)cc1F)C1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001633867857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633867857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633867857 none O=C(c1c(F)cc(F)cc1F)C1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 15, 1, 1, 15, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 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] 0 hydrogens 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, 7, 30, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7, 7, 4, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 34, 34, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/669 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1c(F)cc(F)cc1F)C1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001633867857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633867857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633867857 none O=C(c1c(F)cc(F)cc1F)C1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 15, 1, 1, 15, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 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] 0 hydrogens 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, 4, 28, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633867857 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 Building ZINC001633867857 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633867857 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 668) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c1c(F)cc(F)cc1F)C1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001633867857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633867857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633867857 none O=C(c1c(F)cc(F)cc1F)C1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 15, 1, 1, 15, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 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] 0 hydrogens 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, 7, 30, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7, 7, 4, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 34, 34, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 669) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(c1c(F)cc(F)cc1F)C1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001633867857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633867857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001633867857 none O=C(c1c(F)cc(F)cc1F)C1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 15, 1, 1, 15, 1, 1, 15, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 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] 0 hydrogens 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, 4, 28, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633867857 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633867857 Building ZINC001633884419 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633884419 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/670 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/670' -> `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])c2ccc(O)cc2)[C@H](c2ccccc2Cl)C1) `ZINC001633884419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633884419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633884419 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@H](c2ccccc2Cl)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 12, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 12, 23, 12, 12, 12, 9, 2, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 13, 13, 12, 13, 13, 13, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 4, 2, 2, 13, 13, 13, 13, 12, 12] 100 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, 55]) total number of confs: 126 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/671 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/671' -> `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])c2ccc(O)cc2)[C@H](c2ccccc2Cl)C1) `ZINC001633884419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633884419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633884419 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@H](c2ccccc2Cl)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 12, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 22, 10, 22, 10, 10, 10, 7, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 14, 14, 10, 14, 14, 14, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 10, 10, 10, 10, 2, 2, 4, 2, 2, 14, 14, 14, 14, 10, 10] 100 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, 55]) total number of confs: 131 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633884419 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 Building ZINC001633884419 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633884419 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 670) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@H](c2ccccc2Cl)C1) `ZINC001633884419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633884419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633884419 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@H](c2ccccc2Cl)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 12, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 12, 23, 12, 12, 12, 9, 2, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 13, 13, 12, 13, 13, 13, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 4, 2, 2, 13, 13, 13, 13, 12, 12] 100 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, 55]) total number of confs: 126 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 671) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@H](c2ccccc2Cl)C1) `ZINC001633884419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633884419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633884419 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@H](c2ccccc2Cl)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 12, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 22, 10, 22, 10, 10, 10, 7, 2, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 14, 14, 10, 14, 14, 14, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 10, 10, 10, 10, 2, 2, 4, 2, 2, 14, 14, 14, 14, 10, 10] 100 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, 55]) total number of confs: 131 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633884419 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884419 Building ZINC001633884420 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633884420 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/672 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/672' -> `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])c2ccc(O)cc2)[C@@H](c2ccccc2Cl)C1) `ZINC001633884420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633884420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633884420 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@@H](c2ccccc2Cl)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 12, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 48, 49, 49, 24, 9, 24, 9, 9, 9, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 12, 12, 9, 12, 12, 12, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 9, 9, 9, 2, 2, 4, 2, 2, 12, 12, 9, 12, 9, 9] 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 129 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/673 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/673' -> `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])c2ccc(O)cc2)[C@@H](c2ccccc2Cl)C1) `ZINC001633884420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633884420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633884420 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@@H](c2ccccc2Cl)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 12, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 25, 11, 25, 11, 11, 11, 8, 1, 8, 1, 1, 1, 2, 2, 1, 2, 2, 2, 11, 11, 11, 12, 12, 11, 12, 12, 12, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2, 4, 2, 2, 12, 12, 11, 12, 11, 11] 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633884420 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 Building ZINC001633884420 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633884420 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 672) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@@H](c2ccccc2Cl)C1) `ZINC001633884420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633884420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633884420 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)[C@@H](c2ccccc2Cl)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 12, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 48, 49, 49, 24, 9, 24, 9, 9, 9, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 12, 12, 9, 12, 12, 12, 9, 49, 49, 49, 49, 49, 49, 49, 49, 49, 9, 9, 9, 9, 2, 2, 4, 2, 2, 12, 12, 9, 12, 9, 9] 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 129 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 673) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@@H](c2ccccc2Cl)C1) `ZINC001633884420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633884420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633884420 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)[C@@H](c2ccccc2Cl)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 12, 1, 1, 5, 7, 1, 1, 1, 1, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 25, 11, 25, 11, 11, 11, 8, 1, 8, 1, 1, 1, 2, 2, 1, 2, 2, 2, 11, 11, 11, 12, 12, 11, 12, 12, 12, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2, 4, 2, 2, 12, 12, 11, 12, 11, 11] 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633884420 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633884420 Building ZINC001633964991 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633964991 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/674 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@H](O)c1ccc(Cl)cc1) `ZINC001633964991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633964991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964991 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 4, 7, 7, 2, 2, 1, 1, 1, 1, 6, 6, 6, 14, 14, 28, 27, 14, 33, 33, 33, 37, 37, 33, 33, 37, 37, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 99, 37, 37, 37, 37] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 335 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/675 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@H](O)c1ccc(Cl)cc1) `ZINC001633964991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633964991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964991 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 1, 1, 1, 1, 6, 6, 6, 12, 12, 25, 25, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 8, 8, 3, 8, 8, 2, 2, 2, 6, 25, 25, 25, 25, 25, 25, 25, 93, 31, 31, 31, 31] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 293 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633964991 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 Building ZINC001633964991 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633964991 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 674) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@H](O)c1ccc(Cl)cc1) `ZINC001633964991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633964991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964991 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 4, 7, 7, 2, 2, 1, 1, 1, 1, 6, 6, 6, 14, 14, 28, 27, 14, 33, 33, 33, 37, 37, 33, 33, 37, 37, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 99, 37, 37, 37, 37] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 335 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 675) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@H](O)c1ccc(Cl)cc1) `ZINC001633964991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633964991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964991 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 1, 1, 1, 1, 6, 6, 6, 12, 12, 25, 25, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 8, 8, 3, 8, 8, 2, 2, 2, 6, 25, 25, 25, 25, 25, 25, 25, 93, 31, 31, 31, 31] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 293 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633964991 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964991 Building ZINC001633964992 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633964992 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/676 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@H](O)c1ccc(Cl)cc1) `ZINC001633964992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633964992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964992 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 22, 22, 9, 27, 27, 27, 29, 29, 27, 27, 29, 29, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 5, 22, 22, 22, 22, 22, 22, 22, 81, 29, 29, 29, 29] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 281 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/677 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@H](O)c1ccc(Cl)cc1) `ZINC001633964992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633964992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964992 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 6, 13, 13, 33, 33, 13, 33, 33, 33, 34, 34, 33, 33, 34, 34, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 99, 34, 34, 34, 34] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 346 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633964992 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 Building ZINC001633964992 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633964992 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 676) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@H](O)c1ccc(Cl)cc1) `ZINC001633964992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633964992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964992 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 22, 22, 9, 27, 27, 27, 29, 29, 27, 27, 29, 29, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 5, 22, 22, 22, 22, 22, 22, 22, 81, 29, 29, 29, 29] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 281 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 677) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@H](O)c1ccc(Cl)cc1) `ZINC001633964992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633964992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964992 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 6, 13, 13, 33, 33, 13, 33, 33, 33, 34, 34, 33, 33, 34, 34, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 99, 34, 34, 34, 34] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 346 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633964992 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964992 Building ZINC001633964993 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633964993 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/678 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@@H](O)c1ccc(Cl)cc1) `ZINC001633964993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633964993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964993 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 6, 13, 13, 33, 33, 13, 33, 33, 33, 34, 34, 33, 33, 34, 34, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 99, 34, 34, 34, 34] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 345 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/679 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@@H](O)c1ccc(Cl)cc1) `ZINC001633964993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633964993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964993 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 5, 11, 11, 22, 22, 11, 29, 29, 29, 31, 31, 31, 31, 31, 31, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 3, 5, 22, 22, 22, 22, 22, 22, 22, 87, 31, 31, 31, 31] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 285 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633964993 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 Building ZINC001633964993 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633964993 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 678) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@@H](O)c1ccc(Cl)cc1) `ZINC001633964993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633964993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964993 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 6, 13, 13, 33, 33, 13, 33, 33, 33, 34, 34, 33, 33, 34, 34, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 33, 33, 33, 33, 33, 33, 33, 99, 34, 34, 34, 34] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 345 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 679) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@@H](O)c1ccc(Cl)cc1) `ZINC001633964993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633964993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964993 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)[C@@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 5, 11, 11, 22, 22, 11, 29, 29, 29, 31, 31, 31, 31, 31, 31, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 3, 5, 22, 22, 22, 22, 22, 22, 22, 87, 31, 31, 31, 31] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 285 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633964993 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964993 Building ZINC001633964994 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633964994 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/680 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@@H](O)c1ccc(Cl)cc1) `ZINC001633964994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633964994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964994 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 1, 1, 1, 1, 6, 6, 6, 11, 11, 24, 24, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 2, 6, 24, 24, 24, 24, 24, 24, 24, 93, 31, 31, 31, 31] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 291 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/681 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@@H](O)c1ccc(Cl)cc1) `ZINC001633964994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633964994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964994 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 1, 1, 1, 1, 6, 6, 6, 14, 14, 27, 28, 14, 33, 33, 33, 37, 37, 33, 33, 37, 37, 2, 2, 2, 7, 7, 4, 7, 7, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 99, 37, 37, 37, 37] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 339 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633964994 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 Building ZINC001633964994 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633964994 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 680) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@@H](O)c1ccc(Cl)cc1) `ZINC001633964994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633964994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964994 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 1, 1, 1, 1, 6, 6, 6, 11, 11, 24, 24, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 2, 6, 24, 24, 24, 24, 24, 24, 24, 93, 31, 31, 31, 31] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 291 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 681) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@@H](O)c1ccc(Cl)cc1) `ZINC001633964994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633964994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001633964994 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)[C@@H](O)c1ccc(Cl)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] 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, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 1, 1, 1, 1, 6, 6, 6, 14, 14, 27, 28, 14, 33, 33, 33, 37, 37, 33, 33, 37, 37, 2, 2, 2, 7, 7, 4, 7, 7, 2, 2, 2, 6, 28, 28, 28, 28, 28, 28, 28, 99, 37, 37, 37, 37] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 339 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001633964994 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001633964994 Building ZINC001634048553 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634048553 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/682 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H](O)c1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634048553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634048553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001634048553 none O=C(NCC[C@@H](O)c1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 12, 24, 27, 27, 44, 44, 42, 44, 44, 44, 44, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 19, 19, 81, 44, 44, 44, 6, 6] 150 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]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/683 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H](O)c1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634048553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634048553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001634048553 none O=C(NCC[C@@H](O)c1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 12, 20, 22, 22, 39, 39, 36, 39, 39, 39, 39, 1, 1, 1, 6, 6, 6, 6, 6, 2, 15, 15, 17, 17, 66, 39, 39, 39, 6, 6] 150 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]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634048553 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 Building ZINC001634048553 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634048553 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 682) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(NCC[C@@H](O)c1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634048553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634048553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001634048553 none O=C(NCC[C@@H](O)c1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 12, 24, 27, 27, 44, 44, 42, 44, 44, 44, 44, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 19, 19, 81, 44, 44, 44, 6, 6] 150 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]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 683) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(NCC[C@@H](O)c1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634048553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634048553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001634048553 none O=C(NCC[C@@H](O)c1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 12, 20, 22, 22, 39, 39, 36, 39, 39, 39, 39, 1, 1, 1, 6, 6, 6, 6, 6, 2, 15, 15, 17, 17, 66, 39, 39, 39, 6, 6] 150 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]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634048553 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048553 Building ZINC001634048554 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634048554 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/684 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H](O)c1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634048554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634048554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001634048554 none O=C(NCC[C@H](O)c1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 12, 20, 22, 22, 39, 39, 36, 39, 39, 39, 39, 1, 1, 1, 6, 6, 6, 6, 6, 2, 15, 15, 17, 17, 66, 39, 39, 39, 6, 6] 150 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]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/685 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H](O)c1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634048554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634048554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001634048554 none O=C(NCC[C@H](O)c1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 12, 24, 27, 27, 44, 44, 42, 44, 44, 44, 44, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 19, 19, 81, 44, 44, 44, 6, 6] 150 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]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634048554 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 Building ZINC001634048554 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634048554 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 684) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H](O)c1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634048554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634048554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001634048554 none O=C(NCC[C@H](O)c1ccc(Cl)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 12, 20, 22, 22, 39, 39, 36, 39, 39, 39, 39, 1, 1, 1, 6, 6, 6, 6, 6, 2, 15, 15, 17, 17, 66, 39, 39, 39, 6, 6] 150 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]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 685) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H](O)c1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634048554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634048554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001634048554 none O=C(NCC[C@H](O)c1ccc(Cl)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 1, 1, 16, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 12, 24, 27, 27, 44, 44, 42, 44, 44, 44, 44, 1, 1, 1, 6, 6, 6, 6, 6, 3, 16, 16, 19, 19, 81, 44, 44, 44, 6, 6] 150 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]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634048554 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634048554 Building ZINC001634264885 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634264885 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/686 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)CC2)n1) `ZINC001634264885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634264885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001634264885 none COc1ccccc1c1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 23, 42, 42, 42, 42, 42, 42, 42, 23, 23, 4, 4, 4, 4, 4, 2, 2, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/687 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1c1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)CC2)n1) `ZINC001634264885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634264885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001634264885 none COc1ccccc1c1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 26, 26, 26, 26, 26, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 26, 26, 4, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [44, 45, 17, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634264885 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 Building ZINC001634264885 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634264885 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 686) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1c1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)CC2)n1) `ZINC001634264885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634264885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001634264885 none COc1ccccc1c1ccnc(C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 23, 23, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 23, 42, 42, 42, 42, 42, 42, 42, 23, 23, 4, 4, 4, 4, 4, 2, 2, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 687) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccccc1c1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)CC2)n1) `ZINC001634264885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634264885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001634264885 none COc1ccccc1c1ccnc(C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 26, 26, 26, 26, 26, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 26, 26, 4, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [44, 45, 17, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634264885 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634264885 Building ZINC001634307826 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634307826 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/688 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)c(Br)c3)C2)cc1Cl) `ZINC001634307826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634307826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634307826 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)c(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 26, 26, 19, 26, 26, 26, 26, 5, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 26, 26, 26, 5, 5, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/689 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)c(Br)c3)C2)cc1Cl) `ZINC001634307826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634307826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634307826 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)c(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 25, 25, 13, 25, 25, 25, 25, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 25, 25, 25, 4, 4, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634307826 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 Building ZINC001634307826 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634307826 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 688) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)c(Br)c3)C2)cc1Cl) `ZINC001634307826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634307826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634307826 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)c(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 26, 26, 19, 26, 26, 26, 26, 5, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 26, 26, 26, 5, 5, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 689) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)c(Br)c3)C2)cc1Cl) `ZINC001634307826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634307826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634307826 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)c(Br)c3)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 17, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 25, 25, 13, 25, 25, 25, 25, 4, 2, 2, 2, 4, 4, 4, 2, 2, 1, 4, 4, 25, 25, 25, 4, 4, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634307826 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634307826 Building ZINC001634369621 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634369621 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/690 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)nc3cc(Br)ccc32)cc1) `ZINC001634369621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634369621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001634369621 none Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)nc3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 21, 21, 9, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 9, 8, 8, 8, 8, 8, 8, 21, 21, 21, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/691 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cccn3C)nc3cc(Br)ccc32)cc1) `ZINC001634369621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634369621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001634369621 none Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cccn3C)nc3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 21, 21, 9, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 9, 8, 8, 8, 8, 8, 8, 21, 21, 21, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634369621 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 Building ZINC001634369621 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634369621 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 690) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)nc3cc(Br)ccc32)cc1) `ZINC001634369621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634369621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001634369621 none Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cccn3C)nc3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 21, 21, 9, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 9, 8, 8, 8, 8, 8, 8, 21, 21, 21, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 691) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cccn3C)nc3cc(Br)ccc32)cc1) `ZINC001634369621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634369621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001634369621 none Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cccn3C)nc3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 21, 21, 9, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 9, 8, 8, 8, 8, 8, 8, 21, 21, 21, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634369621 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634369621 Building ZINC001634375108 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634375108 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/692 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2sc(CC(N)=O)cc2Br)cc1) `ZINC001634375108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634375108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001634375108 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2sc(CC(N)=O)cc2Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 5, 1, 8, 11, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 10, 10, 10, 17, 17, 17, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 17, 17, 17, 10, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/693 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(c2sc(CC(N)=O)cc2Br)cc1) `ZINC001634375108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634375108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001634375108 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(c2sc(CC(N)=O)cc2Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 5, 1, 8, 11, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 12, 12, 12, 17, 17, 17, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 17, 17, 17, 12, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634375108 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 Building ZINC001634375108 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634375108 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 692) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2sc(CC(N)=O)cc2Br)cc1) `ZINC001634375108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634375108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001634375108 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2sc(CC(N)=O)cc2Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 5, 1, 8, 11, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 2, 2, 10, 10, 10, 17, 17, 17, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 17, 17, 17, 10, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 693) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(c2sc(CC(N)=O)cc2Br)cc1) `ZINC001634375108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634375108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001634375108 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(c2sc(CC(N)=O)cc2Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 14, 1, 5, 1, 8, 11, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 12, 12, 12, 17, 17, 17, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 17, 17, 17, 17, 12, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634375108 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634375108 Building ZINC001634381777 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634381777 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/694 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001634381777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634381777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001634381777 none CC(C)(C)OC(=O)N1CCC2(CCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 17, 32, 17, 17, 17, 17, 17, 17, 4, 2, 7, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 2, 1, 2, 17, 17, 17, 17] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/695 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001634381777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634381777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001634381777 none CC(C)(C)OC(=O)N1CCC2(CCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 20, 34, 20, 20, 20, 20, 20, 20, 6, 2, 10, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 20, 20, 20, 20, 20, 20, 20, 20, 3, 1, 3, 20, 20, 20, 20] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634381777 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 Building ZINC001634381777 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634381777 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 694) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC2(CCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001634381777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634381777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001634381777 none CC(C)(C)OC(=O)N1CCC2(CCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 17, 32, 17, 17, 17, 17, 17, 17, 4, 2, 7, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 2, 1, 2, 17, 17, 17, 17] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 695) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC2(CCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001634381777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634381777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001634381777 none CC(C)(C)OC(=O)N1CCC2(CCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 20, 34, 20, 20, 20, 20, 20, 20, 6, 2, 10, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 20, 20, 20, 20, 20, 20, 20, 20, 3, 1, 3, 20, 20, 20, 20] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634381777 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634381777 Building ZINC001634572963 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634572963 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/696 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2c(Br)cccc2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001634572963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634572963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001634572963 none O=C(N1CCOc2c(Br)cccc2C1)[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.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 17, 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] dock color type numbers: [6, 9, 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] 0 hydrogens 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, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 46, 46, 46, 46, 46, 46, 46, 46, 46, 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, 30, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/697 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2c(Br)cccc2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001634572963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634572963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001634572963 none O=C(N1CCOc2c(Br)cccc2C1)[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.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 17, 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] dock color type numbers: [6, 9, 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] 0 hydrogens 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, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 2, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634572963 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 Building ZINC001634572963 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634572963 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 696) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCOc2c(Br)cccc2C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001634572963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634572963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001634572963 none O=C(N1CCOc2c(Br)cccc2C1)[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.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 17, 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] dock color type numbers: [6, 9, 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] 0 hydrogens 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, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 46, 46, 46, 46, 46, 46, 46, 46, 46, 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, 30, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 697) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCOc2c(Br)cccc2C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001634572963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634572963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001634572963 none O=C(N1CCOc2c(Br)cccc2C1)[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.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 17, 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] dock color type numbers: [6, 9, 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] 0 hydrogens 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, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 2, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634572963 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634572963 Building ZINC001634595398 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634595398 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/698 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@@H]2C2CC2)cc1Cl) `ZINC001634595398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634595398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634595398 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@@H]2C2CC2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 14, 6, 6, 14, 6, 6, 6, 6, 6, 8, 8, 6, 6, 6, 13, 13, 13, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/699 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@@H]2C2CC2)cc1Cl) `ZINC001634595398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634595398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634595398 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@@H]2C2CC2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 5, 5, 5, 5, 13, 5, 5, 14, 5, 5, 5, 5, 5, 7, 7, 6, 6, 6, 13, 13, 13, 6, 6, 5, 5, 5, 5, 5, 13, 13, 13, 14, 14, 14, 5, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634595398 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 Building ZINC001634595398 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634595398 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 698) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@@H]2C2CC2)cc1Cl) `ZINC001634595398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634595398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634595398 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@@H]2C2CC2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 14, 6, 6, 14, 6, 6, 6, 6, 6, 8, 8, 6, 6, 6, 13, 13, 13, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 699) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@@H]2C2CC2)cc1Cl) `ZINC001634595398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634595398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634595398 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@@H]2C2CC2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 5, 5, 5, 5, 13, 5, 5, 14, 5, 5, 5, 5, 5, 7, 7, 6, 6, 6, 13, 13, 13, 6, 6, 5, 5, 5, 5, 5, 13, 13, 13, 14, 14, 14, 5, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634595398 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595398 Building ZINC001634595399 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634595399 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/700 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@H]2C2CC2)cc1Cl) `ZINC001634595399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634595399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634595399 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@H]2C2CC2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 13, 5, 5, 14, 5, 5, 5, 5, 5, 8, 8, 6, 6, 6, 14, 14, 14, 6, 6, 5, 5, 5, 5, 5, 13, 13, 13, 14, 14, 14, 5, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/369383/xbb-8058088.28/working/building/ZINC001634595399 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/701 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@H]2C2CC2)cc1Cl) `ZINC001634595399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634595399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634595399 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@H]2C2CC2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 16, 7, 7, 18, 7, 7, 7, 7, 7, 9, 9, 4, 4, 4, 11, 11, 11, 4, 4, 7, 7, 7, 7, 7, 16, 16, 16, 18, 18, 18, 7, 9, 9, 9, 9, 9, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634595399 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399 Building ZINC001634595399 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634595399 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 700) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@H]2C2CC2)cc1Cl) `ZINC001634595399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634595399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634595399 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@H]2C2CC2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 13, 5, 5, 14, 5, 5, 5, 5, 5, 8, 8, 6, 6, 6, 14, 14, 14, 6, 6, 5, 5, 5, 5, 5, 13, 13, 13, 14, 14, 14, 5, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/369383/xbb-8058088.28/working/building/ZINC001634595399 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 701) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@H]2C2CC2)cc1Cl) `ZINC001634595399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634595399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001634595399 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(OC)c(OC)cc3[C@H]2C2CC2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 5, 7, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 16, 7, 7, 18, 7, 7, 7, 7, 7, 9, 9, 4, 4, 4, 11, 11, 11, 4, 4, 7, 7, 7, 7, 7, 16, 16, 16, 18, 18, 18, 7, 9, 9, 9, 9, 9, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634595399 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634595399 Building ZINC001634674599 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634674599 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/702 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]12CN(Cc3ccccc3)C[C@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634674599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674599 none C[C@]12CN(Cc3ccccc3)C[C@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 33, 38, 38, 38, 38, 38, 15, 15, 15, 15, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 33, 33, 38, 38, 38, 38, 38, 15, 15, 15, 15, 15, 15, 15, 5, 5, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/703 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]12CN(Cc3ccccc3)C[C@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634674599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674599 none C[C@]12CN(Cc3ccccc3)C[C@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 29, 32, 32, 32, 32, 32, 14, 14, 14, 14, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 29, 29, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 14, 14, 6, 6, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634674599 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 Building ZINC001634674599 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634674599 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 702) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@]12CN(Cc3ccccc3)C[C@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634674599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674599 none C[C@]12CN(Cc3ccccc3)C[C@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 33, 38, 38, 38, 38, 38, 15, 15, 15, 15, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 33, 33, 38, 38, 38, 38, 38, 15, 15, 15, 15, 15, 15, 15, 5, 5, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 703) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@]12CN(Cc3ccccc3)C[C@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634674599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674599 none C[C@]12CN(Cc3ccccc3)C[C@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 29, 32, 32, 32, 32, 32, 14, 14, 14, 14, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 29, 29, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 14, 14, 6, 6, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634674599 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674599 Building ZINC001634674600 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634674600 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/704 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634674600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674600 none C[C@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 12, 12, 12, 12, 12, 12, 12, 2, 2, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/705 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634674600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674600 none C[C@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 34, 35, 35, 34, 35, 35, 11, 11, 11, 11, 3, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 34, 34, 35, 35, 34, 35, 35, 11, 11, 11, 11, 11, 11, 11, 3, 3, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634674600 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 Building ZINC001634674600 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634674600 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 704) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634674600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674600 none C[C@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 12, 12, 12, 12, 12, 12, 12, 2, 2, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 705) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634674600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674600 none C[C@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 34, 35, 35, 34, 35, 35, 11, 11, 11, 11, 3, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 34, 34, 35, 35, 34, 35, 35, 11, 11, 11, 11, 11, 11, 11, 3, 3, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634674600 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674600 Building ZINC001634674601 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634674601 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/706 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634674601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674601 none C[C@@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 32, 35, 35, 35, 35, 35, 13, 13, 13, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 32, 32, 35, 35, 35, 35, 35, 13, 13, 13, 13, 13, 13, 13, 6, 6, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/707 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634674601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674601 none C[C@@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 32, 37, 37, 33, 37, 37, 15, 15, 15, 15, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 32, 32, 37, 37, 37, 37, 37, 15, 15, 15, 15, 15, 15, 15, 6, 6, 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634674601 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 Building ZINC001634674601 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634674601 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 706) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634674601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674601 none C[C@@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 32, 35, 35, 35, 35, 35, 13, 13, 13, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 32, 32, 35, 35, 35, 35, 35, 13, 13, 13, 13, 13, 13, 13, 6, 6, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 707) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2) `ZINC001634674601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634674601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001634674601 none C[C@@]12CN(Cc3ccccc3)C[C@@]1(C)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C2 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.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', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 32, 37, 37, 33, 37, 37, 15, 15, 15, 15, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 32, 32, 37, 37, 37, 37, 37, 15, 15, 15, 15, 15, 15, 15, 6, 6, 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634674601 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634674601 Building ZINC001634742471 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634742471 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/708 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Br)c(F)c1) `ZINC001634742471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634742471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001634742471 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Br)c(F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 37, 49, 49, 49, 49, 49, 49, 49, 12, 12, 2, 3, 1, 3, 49, 49, 49] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/709 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Br)c(F)c1) `ZINC001634742471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634742471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001634742471 none O=C(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Br)c(F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 36, 49, 49, 49, 49, 49, 49, 49, 12, 12, 2, 3, 1, 3, 49, 49, 49] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634742471 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 Building ZINC001634742471 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634742471 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 708) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Br)c(F)c1) `ZINC001634742471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634742471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001634742471 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Br)c(F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 37, 49, 49, 49, 49, 49, 49, 49, 12, 12, 2, 3, 1, 3, 49, 49, 49] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 709) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Br)c(F)c1) `ZINC001634742471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634742471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001634742471 none O=C(CNC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Br)c(F)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 36, 49, 49, 49, 49, 49, 49, 49, 12, 12, 2, 3, 1, 3, 49, 49, 49] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634742471 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634742471 Building ZINC001634761758 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634761758 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/710 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Cc2ccc(F)c(F)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634761758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634761758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001634761758 none O=C(N1CCC(Cc2ccc(F)c(F)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 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] 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] 0 hydrogens need rotated 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, 16, 33, 33, 33, 33, 33, 33, 33, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 16, 16, 33, 33, 33, 7, 7, 7, 7, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 94 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/711 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Cc2ccc(F)c(F)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634761758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634761758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001634761758 none O=C(N1CCC(Cc2ccc(F)c(F)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 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] 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] 0 hydrogens need 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, 6, 6, 6, 6, 15, 30, 30, 30, 30, 30, 30, 30, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 15, 15, 30, 30, 30, 6, 6, 6, 6, 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]) total number of confs: 86 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634761758 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 Building ZINC001634761758 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634761758 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 710) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CCC(Cc2ccc(F)c(F)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634761758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634761758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001634761758 none O=C(N1CCC(Cc2ccc(F)c(F)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 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] 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] 0 hydrogens need rotated 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, 16, 33, 33, 33, 33, 33, 33, 33, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 16, 16, 33, 33, 33, 7, 7, 7, 7, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 94 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 711) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CCC(Cc2ccc(F)c(F)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001634761758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634761758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001634761758 none O=C(N1CCC(Cc2ccc(F)c(F)c2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 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] 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] 0 hydrogens need 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, 6, 6, 6, 6, 15, 30, 30, 30, 30, 30, 30, 30, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 15, 15, 30, 30, 30, 6, 6, 6, 6, 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]) total number of confs: 86 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634761758 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634761758 Building ZINC001634911190 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634911190 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/712 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 29, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 2, 3, 16, 8, 16, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/713 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 29, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 16, 16, 16, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 247 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/714 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/714' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911190.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 8, 17, 17, 17, 8, 17, 17, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 4, 1, 4, 17, 17, 17, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 257 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/715 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/715' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911190.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 8, 17, 17, 17, 8, 17, 17, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 4, 1, 4, 17, 8, 17, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634911190 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 Building ZINC001634911190 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634911190 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 712) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 29, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 2, 3, 16, 8, 16, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 713) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 29, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 16, 16, 16, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 247 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 714) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911190.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 8, 17, 17, 17, 8, 17, 17, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 4, 1, 4, 17, 17, 17, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 257 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 715) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911190.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 8, 17, 17, 17, 8, 17, 17, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 4, 1, 4, 17, 8, 17, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634911190 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 Building ZINC001634911190 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634911190 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 712) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 29, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 2, 3, 16, 8, 16, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 713) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 29, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 16, 16, 16, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 247 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 714) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911190.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 8, 17, 17, 17, 8, 17, 17, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 4, 1, 4, 17, 17, 17, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 257 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 715) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911190.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 8, 17, 17, 17, 8, 17, 17, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 4, 1, 4, 17, 8, 17, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634911190 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 Building ZINC001634911190 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634911190 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 712) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 29, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 2, 3, 16, 8, 16, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 236 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 713) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 29, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 16, 16, 16, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 247 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 714) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911190.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 8, 17, 17, 17, 8, 17, 17, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 4, 1, 4, 17, 17, 17, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 257 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 715) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911190.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634911190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911190 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 8, 17, 17, 17, 8, 17, 17, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 4, 1, 4, 17, 8, 17, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634911190 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911190 Building ZINC001634911191 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634911191 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/716 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 16, 16, 16, 27, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 4, 3, 1, 3, 16, 16, 16, 38, 38, 38, 38, 114, 38, 38, 38, 38] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/717 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 27, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 4, 3, 1, 3, 16, 8, 16, 38, 38, 38, 38, 114, 38, 38, 38, 38] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 230 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/718 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/718' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911191.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 15, 8, 15, 15, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 15, 15, 15, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 244 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/719 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/719' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911191.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 15, 8, 15, 15, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 15, 8, 15, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634911191 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 Building ZINC001634911191 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634911191 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 716) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 16, 16, 16, 27, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 4, 3, 1, 3, 16, 16, 16, 38, 38, 38, 38, 114, 38, 38, 38, 38] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 717) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 27, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 4, 3, 1, 3, 16, 8, 16, 38, 38, 38, 38, 114, 38, 38, 38, 38] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 230 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 718) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911191.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 15, 8, 15, 15, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 15, 15, 15, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 244 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 719) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911191.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 15, 8, 15, 15, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 15, 8, 15, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634911191 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 Building ZINC001634911191 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634911191 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 716) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 16, 16, 16, 27, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 4, 3, 1, 3, 16, 16, 16, 38, 38, 38, 38, 114, 38, 38, 38, 38] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 717) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 27, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 4, 3, 1, 3, 16, 8, 16, 38, 38, 38, 38, 114, 38, 38, 38, 38] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 230 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 718) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911191.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 15, 8, 15, 15, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 15, 15, 15, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 244 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 719) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911191.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 15, 8, 15, 15, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 15, 8, 15, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634911191 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 Building ZINC001634911191 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001634911191 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 716) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 16, 16, 16, 27, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 4, 3, 1, 3, 16, 16, 16, 38, 38, 38, 38, 114, 38, 38, 38, 38] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 717) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 16, 16, 16, 8, 16, 16, 27, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 4, 3, 1, 3, 16, 8, 16, 38, 38, 38, 38, 114, 38, 38, 38, 38] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 230 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 718) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1) `ZINC001634911191.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 15, 8, 15, 15, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 15, 15, 15, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 244 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 719) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1) `ZINC001634911191.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001634911191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001634911191 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1cc(F)ccc1[N@]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 15, 15, 15, 8, 15, 15, 28, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 4, 3, 1, 3, 15, 8, 15, 39, 39, 39, 39, 117, 39, 39, 39, 39] 150 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634911191 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634911191 Building ZINC001634952735 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634952735 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/720 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(O)cc(Br)cc1Cl) `ZINC001634952735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634952735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001634952735 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(O)cc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 12, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 8, 8, 8, 29, 29, 29, 16, 29, 29, 29, 29, 4, 4, 4, 14, 14, 6, 14, 14, 4, 4, 4, 8, 58, 29, 29] 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]) total number of confs: 200 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/721 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(O)cc(Br)cc1Cl) `ZINC001634952735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634952735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001634952735 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(O)cc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 12, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 8, 8, 8, 29, 29, 29, 16, 29, 29, 29, 29, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 8, 58, 29, 29] 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]) total number of confs: 196 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634952735 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 Building ZINC001634952735 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634952735 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 720) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(O)cc(Br)cc1Cl) `ZINC001634952735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634952735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001634952735 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(O)cc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 12, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 8, 8, 8, 29, 29, 29, 16, 29, 29, 29, 29, 4, 4, 4, 14, 14, 6, 14, 14, 4, 4, 4, 8, 58, 29, 29] 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]) total number of confs: 200 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 721) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(O)cc(Br)cc1Cl) `ZINC001634952735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634952735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001634952735 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(O)cc(Br)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 12, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 8, 8, 8, 29, 29, 29, 16, 29, 29, 29, 29, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 8, 58, 29, 29] 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]) total number of confs: 196 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001634952735 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001634952735 Building ZINC001635058134 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635058134 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/722 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635058134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635058134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001635058134 none CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=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.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', '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, 8, 5, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 20, 29, 8, 4, 4, 3, 2, 3, 5, 6, 6, 6, 6, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 8, 8, 4, 4, 4, 4, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/723 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635058134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635058134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001635058134 none CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=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.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', '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, 8, 5, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 26, 7, 3, 3, 2, 2, 2, 4, 7, 7, 7, 7, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 18, 7, 7, 3, 3, 3, 3, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635058134 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 Building ZINC001635058134 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635058134 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 722) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635058134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635058134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001635058134 none CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=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.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', '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, 8, 5, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 20, 29, 8, 4, 4, 3, 2, 3, 5, 6, 6, 6, 6, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 8, 8, 4, 4, 4, 4, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 723) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635058134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635058134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001635058134 none CC(C)(C)OC(=O)NCCCN(CC1CCCC1)C(=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.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', '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, 8, 5, 5, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 26, 7, 3, 3, 2, 2, 2, 4, 7, 7, 7, 7, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 18, 7, 7, 3, 3, 3, 3, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635058134 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635058134 Building ZINC001635064191 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635064191 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/724 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCNS(=O)(=O)c1ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001635064191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635064191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635064191 none CCCCNS(=O)(=O)c1ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 14, 10, 8, 10, 10, 8, 4, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 50, 50, 50, 50, 50, 50, 50, 36, 36, 14, 6, 8, 8, 8, 8, 2, 2, 1, 2, 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, 44, 45, 46, 47]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/725 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCNS(=O)(=O)c1ccc(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001635064191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635064191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635064191 none CCCCNS(=O)(=O)c1ccc(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 14, 10, 8, 10, 10, 8, 2, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 50, 50, 50, 50, 50, 50, 50, 35, 35, 14, 4, 8, 8, 8, 8, 2, 2, 1, 2, 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, 44, 45, 46, 47]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635064191 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 Building ZINC001635064191 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635064191 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 724) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCCCNS(=O)(=O)c1ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001635064191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635064191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635064191 none CCCCNS(=O)(=O)c1ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 14, 10, 8, 10, 10, 8, 4, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 50, 50, 50, 50, 50, 50, 50, 36, 36, 14, 6, 8, 8, 8, 8, 2, 2, 1, 2, 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, 44, 45, 46, 47]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 725) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCCCNS(=O)(=O)c1ccc(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1) `ZINC001635064191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635064191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635064191 none CCCCNS(=O)(=O)c1ccc(C)c(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', '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, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 14, 10, 8, 10, 10, 8, 2, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 8, 50, 50, 50, 50, 50, 50, 50, 35, 35, 14, 4, 8, 8, 8, 8, 2, 2, 1, 2, 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, 44, 45, 46, 47]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635064191 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635064191 Building ZINC001635072158 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001635072158 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/726 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 32, 27, 27, 27, 27, 10, 27, 10, 10, 10, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 27, 27, 32, 32, 32, 32, 32, 32, 32, 27, 27, 27, 27, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 27, 27, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/727 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 31, 31, 31, 31, 10, 31, 10, 10, 10, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 31, 31, 36, 36, 36, 36, 36, 36, 36, 31, 31, 31, 31, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 31, 31, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/728 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/728' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 32, 28, 28, 28, 28, 10, 28, 10, 10, 10, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 28, 28, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 10, 10, 10, 10, 5, 5, 10, 10, 10, 10, 28, 28, 28, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/729 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/729' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 32, 28, 28, 28, 28, 9, 28, 9, 9, 9, 4, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 28, 28, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9, 28, 28, 28, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635072158 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 Building ZINC001635072158 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001635072158 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 726) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 32, 27, 27, 27, 27, 10, 27, 10, 10, 10, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 27, 27, 32, 32, 32, 32, 32, 32, 32, 27, 27, 27, 27, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 27, 27, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 727) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 31, 31, 31, 31, 10, 31, 10, 10, 10, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 31, 31, 36, 36, 36, 36, 36, 36, 36, 31, 31, 31, 31, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 31, 31, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 728) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 32, 28, 28, 28, 28, 10, 28, 10, 10, 10, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 28, 28, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 10, 10, 10, 10, 5, 5, 10, 10, 10, 10, 28, 28, 28, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 729) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 32, 28, 28, 28, 28, 9, 28, 9, 9, 9, 4, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 28, 28, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9, 28, 28, 28, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635072158 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 Building ZINC001635072158 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001635072158 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 726) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 32, 27, 27, 27, 27, 10, 27, 10, 10, 10, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 27, 27, 32, 32, 32, 32, 32, 32, 32, 27, 27, 27, 27, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 27, 27, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 727) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 31, 31, 31, 31, 10, 31, 10, 10, 10, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 31, 31, 36, 36, 36, 36, 36, 36, 36, 31, 31, 31, 31, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 31, 31, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 728) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 32, 28, 28, 28, 28, 10, 28, 10, 10, 10, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 28, 28, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 10, 10, 10, 10, 5, 5, 10, 10, 10, 10, 28, 28, 28, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 729) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 32, 28, 28, 28, 28, 9, 28, 9, 9, 9, 4, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 28, 28, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9, 28, 28, 28, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635072158 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 Building ZINC001635072158 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001635072158 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 726) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 32, 27, 27, 27, 27, 10, 27, 10, 10, 10, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 27, 27, 32, 32, 32, 32, 32, 32, 32, 27, 27, 27, 27, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 27, 27, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 727) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 31, 31, 31, 31, 10, 31, 10, 10, 10, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 31, 31, 36, 36, 36, 36, 36, 36, 36, 31, 31, 31, 31, 10, 10, 10, 10, 6, 6, 10, 10, 10, 10, 31, 31, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 728) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 32, 28, 28, 28, 28, 10, 28, 10, 10, 10, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 28, 28, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 10, 10, 10, 10, 5, 5, 10, 10, 10, 10, 28, 28, 28, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 729) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1) `ZINC001635072158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001635072158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001635072158 none CC(C)[C@H]1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 32, 28, 28, 28, 28, 9, 28, 9, 9, 9, 4, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 28, 28, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9, 28, 28, 28, 28] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635072158 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635072158 Building ZINC001635082375 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635082375 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/730 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cc(Br)ccc2OC2(CCC2)C1) `ZINC001635082375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635082375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001635082375 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cc(Br)ccc2OC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 15, 23, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 36, 36, 36, 36, 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]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/731 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cc(Br)ccc2OC2(CCC2)C1) `ZINC001635082375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635082375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001635082375 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cc(Br)ccc2OC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 14, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 3, 3, 3, 3, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 43 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635082375 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 Building ZINC001635082375 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635082375 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 730) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cc(Br)ccc2OC2(CCC2)C1) `ZINC001635082375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635082375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001635082375 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2cc(Br)ccc2OC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 15, 23, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 36, 36, 36, 36, 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]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 731) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cc(Br)ccc2OC2(CCC2)C1) `ZINC001635082375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635082375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001635082375 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1Cc2cc(Br)ccc2OC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 14, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 37, 3, 3, 3, 3, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 43 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635082375 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635082375 Building ZINC001635198527 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635198527 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/732 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001635198527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635198527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001635198527 none CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 36, 36, 29, 18, 29, 18, 18, 18, 18, 13, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 18, 18, 18, 18, 18, 18, 11, 11, 4, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/733 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001635198527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635198527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001635198527 none CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 21, 30, 21, 21, 21, 21, 16, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 21, 21, 13, 13, 4, 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635198527 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 Building ZINC001635198527 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635198527 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 732) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001635198527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635198527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001635198527 none CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 36, 36, 29, 18, 29, 18, 18, 18, 18, 13, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 18, 18, 18, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 18, 18, 18, 18, 18, 18, 11, 11, 4, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 733) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001635198527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635198527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001635198527 none CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 21, 30, 21, 21, 21, 21, 16, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 21, 21, 13, 13, 4, 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635198527 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198527 Building ZINC001635198528 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635198528 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/734 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001635198528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635198528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001635198528 none CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 20, 28, 20, 20, 20, 20, 15, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 20, 20, 20, 20, 12, 12, 4, 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/735 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001635198528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635198528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001635198528 none CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 19, 28, 19, 19, 19, 19, 13, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 19, 19, 19, 19, 36, 36, 36, 36, 36, 36, 36, 36, 36, 19, 19, 19, 19, 19, 19, 11, 11, 4, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635198528 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 Building ZINC001635198528 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635198528 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 734) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001635198528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635198528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001635198528 none CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 20, 28, 20, 20, 20, 20, 15, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 20, 20, 20, 20, 12, 12, 4, 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 735) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F) `ZINC001635198528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635198528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001635198528 none CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C(F)(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 19, 28, 19, 19, 19, 19, 13, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 19, 19, 19, 19, 36, 36, 36, 36, 36, 36, 36, 36, 36, 19, 19, 19, 19, 19, 19, 11, 11, 4, 7, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635198528 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635198528 Building ZINC001635468492 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635468492 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/736 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C[C@H](O)c1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001635468492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635468492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635468492 none CC(C)CN(C[C@H](O)c1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 9, 4, 9, 18, 26, 26, 26, 31, 31, 31, 31, 31, 31, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 78, 31, 31, 31, 31, 9, 9] 150 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]) total number of confs: 224 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/737 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C[C@H](O)c1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001635468492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635468492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635468492 none CC(C)CN(C[C@H](O)c1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 11, 12, 8, 4, 8, 13, 25, 25, 25, 31, 31, 31, 31, 31, 31, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 11, 11, 13, 13, 75, 31, 31, 31, 31, 9, 9] 150 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]) total number of confs: 224 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635468492 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 Building ZINC001635468492 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635468492 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 736) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C[C@H](O)c1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001635468492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635468492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635468492 none CC(C)CN(C[C@H](O)c1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 9, 4, 9, 18, 26, 26, 26, 31, 31, 31, 31, 31, 31, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 78, 31, 31, 31, 31, 9, 9] 150 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]) total number of confs: 224 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 737) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C[C@H](O)c1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001635468492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635468492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635468492 none CC(C)CN(C[C@H](O)c1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 11, 12, 8, 4, 8, 13, 25, 25, 25, 31, 31, 31, 31, 31, 31, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 11, 11, 13, 13, 75, 31, 31, 31, 31, 9, 9] 150 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]) total number of confs: 224 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635468492 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468492 Building ZINC001635468493 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635468493 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/738 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C[C@@H](O)c1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001635468493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635468493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635468493 none CC(C)CN(C[C@@H](O)c1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 11, 12, 9, 5, 9, 17, 25, 25, 25, 27, 27, 25, 25, 27, 27, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 11, 11, 17, 17, 75, 27, 27, 27, 27, 8, 8] 150 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]) total number of confs: 222 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/739 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C[C@@H](O)c1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001635468493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635468493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635468493 none CC(C)CN(C[C@@H](O)c1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 8, 3, 8, 14, 22, 22, 22, 28, 28, 22, 28, 28, 28, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14, 66, 28, 28, 28, 28, 7, 7] 150 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]) total number of confs: 234 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635468493 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 Building ZINC001635468493 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635468493 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 738) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C[C@@H](O)c1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001635468493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635468493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635468493 none CC(C)CN(C[C@@H](O)c1ccc(F)cc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 11, 12, 9, 5, 9, 17, 25, 25, 25, 27, 27, 25, 25, 27, 27, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 11, 11, 17, 17, 75, 27, 27, 27, 27, 8, 8] 150 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]) total number of confs: 222 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 739) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C[C@@H](O)c1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001635468493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635468493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001635468493 none CC(C)CN(C[C@@H](O)c1ccc(F)cc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 7, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 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, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 8, 3, 8, 14, 22, 22, 22, 28, 28, 22, 28, 28, 28, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14, 66, 28, 28, 28, 28, 7, 7] 150 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]) total number of confs: 234 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635468493 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635468493 Building ZINC001635530405 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635530405 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/740 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(CN2CCOCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635530405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635530405 none O=C(Nc1ccc(Cl)c(CN2CCOCC2)c1)[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', 'Cl', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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, 1, 1, 1, 1, 16, 1, 5, 10, 5, 5, 12, 5, 5, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 2, 4, 11, 11, 43, 44, 44, 44, 44, 44, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 11, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/741 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(CN2CCOCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635530405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635530405 none O=C(Nc1ccc(Cl)c(CN2CCOCC2)c1)[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', 'Cl', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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, 1, 1, 1, 1, 16, 1, 5, 10, 5, 5, 12, 5, 5, 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, 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, 7] 0 hydrogens need rotated 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, 42, 42, 42, 42, 42, 42, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 11, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635530405 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 Building ZINC001635530405 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635530405 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 740) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccc(Cl)c(CN2CCOCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635530405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635530405 none O=C(Nc1ccc(Cl)c(CN2CCOCC2)c1)[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', 'Cl', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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, 1, 1, 1, 1, 16, 1, 5, 10, 5, 5, 12, 5, 5, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 2, 4, 11, 11, 43, 44, 44, 44, 44, 44, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 11, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 741) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1ccc(Cl)c(CN2CCOCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635530405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635530405 none O=C(Nc1ccc(Cl)c(CN2CCOCC2)c1)[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', 'Cl', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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, 1, 1, 1, 1, 16, 1, 5, 10, 5, 5, 12, 5, 5, 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, 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, 7] 0 hydrogens need rotated 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, 42, 42, 42, 42, 42, 42, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 11, 11, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 11, 3, 1, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635530405 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635530405 Building ZINC001635669876 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635669876 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/742 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001635669876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635669876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001635669876 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)CN2C(=O)OC(C)(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/743 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001635669876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635669876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001635669876 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)CN2C(=O)OC(C)(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635669876 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 Building ZINC001635669876 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635669876 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 742) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001635669876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635669876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001635669876 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)CN2C(=O)OC(C)(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 743) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001635669876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635669876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001635669876 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC(C)(C)CN2C(=O)OC(C)(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635669876 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669876 Building ZINC001635669877 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635669877 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/744 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001635669877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635669877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001635669877 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)CN2C(=O)OC(C)(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/745 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001635669877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635669877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001635669877 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)CN2C(=O)OC(C)(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635669877 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 Building ZINC001635669877 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635669877 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 744) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001635669877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635669877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001635669877 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)CN2C(=O)OC(C)(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 745) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001635669877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635669877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001635669877 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC(C)(C)CN2C(=O)OC(C)(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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635669877 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635669877 Building ZINC001635765380 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635765380 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/746 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635765380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635765380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635765380 none O=C(N1CCC[C@H](Nc2cccc(Br)c2)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', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 12, 32, 32, 29, 32, 32, 32, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 32, 32, 31, 32, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/747 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635765380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635765380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635765380 none O=C(N1CCC[C@H](Nc2cccc(Br)c2)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', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 13, 34, 34, 34, 34, 34, 34, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635765380 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 Building ZINC001635765380 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635765380 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 746) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635765380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635765380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635765380 none O=C(N1CCC[C@H](Nc2cccc(Br)c2)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', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 12, 32, 32, 29, 32, 32, 32, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 32, 32, 31, 32, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 747) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635765380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635765380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635765380 none O=C(N1CCC[C@H](Nc2cccc(Br)c2)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', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 13, 34, 34, 34, 34, 34, 34, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635765380 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765380 Building ZINC001635765381 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635765381 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/748 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635765381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635765381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635765381 none O=C(N1CCC[C@@H](Nc2cccc(Br)c2)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', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 14, 33, 33, 28, 33, 33, 33, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 14, 33, 33, 33, 33, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/749 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635765381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635765381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635765381 none O=C(N1CCC[C@@H](Nc2cccc(Br)c2)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', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 13, 35, 35, 33, 35, 35, 35, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 13, 35, 35, 35, 35, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635765381 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 Building ZINC001635765381 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635765381 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 748) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635765381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635765381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635765381 none O=C(N1CCC[C@@H](Nc2cccc(Br)c2)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', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 14, 33, 33, 28, 33, 33, 33, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 14, 33, 33, 33, 33, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 749) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@@H](Nc2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001635765381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635765381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001635765381 none O=C(N1CCC[C@@H](Nc2cccc(Br)c2)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', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 13, 35, 35, 33, 35, 35, 35, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 13, 35, 35, 35, 35, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635765381 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635765381 Building ZINC001635846387 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635846387 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/750 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F) `ZINC001635846387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635846387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001635846387 none C[C@@H](CO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 29, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 29, 29, 87, 17, 17, 3, 8, 8, 8, 8, 17] 150 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]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/751 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F) `ZINC001635846387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635846387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001635846387 none C[C@@H](CO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 31, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 31, 31, 93, 17, 17, 3, 7, 7, 7, 7, 17] 150 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]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635846387 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 Building ZINC001635846387 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635846387 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 750) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F) `ZINC001635846387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635846387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001635846387 none C[C@@H](CO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 29, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 29, 29, 87, 17, 17, 3, 8, 8, 8, 8, 17] 150 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]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 751) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F) `ZINC001635846387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635846387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001635846387 none C[C@@H](CO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 31, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 31, 31, 93, 17, 17, 3, 7, 7, 7, 7, 17] 150 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]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635846387 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846387 Building ZINC001635846388 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635846388 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/752 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F) `ZINC001635846388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635846388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001635846388 none C[C@H](CO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 31, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 31, 31, 93, 17, 17, 3, 7, 7, 7, 7, 17] 150 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]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/753 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F) `ZINC001635846388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635846388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001635846388 none C[C@H](CO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 18, 19, 19, 29, 18, 18, 18, 18, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 29, 29, 87, 18, 18, 3, 8, 8, 8, 8, 18] 150 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]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635846388 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 Building ZINC001635846388 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635846388 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 752) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](CO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F) `ZINC001635846388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635846388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001635846388 none C[C@H](CO)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 18, 18, 31, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 31, 31, 93, 17, 17, 3, 7, 7, 7, 7, 17] 150 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]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 753) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H](CO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F) `ZINC001635846388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635846388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001635846388 none C[C@H](CO)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 18, 19, 19, 29, 18, 18, 18, 18, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 29, 29, 87, 18, 18, 3, 8, 8, 8, 8, 18] 150 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]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635846388 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635846388 Building ZINC001635900467 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635900467 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/754 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635900467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635900467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001635900467 none O=C(NC[C@H](CO)Cc1ccc(C(F)(F)F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 15, 40, 34, 43, 38, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 41, 40, 129, 49, 49, 49, 49, 49, 49, 3, 1, 3] 150 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]) total number of confs: 385 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/755 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635900467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635900467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001635900467 none O=C(NC[C@H](CO)Cc1ccc(C(F)(F)F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 14, 38, 35, 41, 36, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 40, 40, 123, 49, 49, 49, 49, 49, 49, 3, 1, 3] 150 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]) total number of confs: 365 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635900467 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 Building ZINC001635900467 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635900467 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 754) grep: /scratch/xiaobo/369383/xbb-8058088.28/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](CO)Cc1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635900467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635900467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001635900467 none O=C(NC[C@H](CO)Cc1ccc(C(F)(F)F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 15, 40, 34, 43, 38, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 41, 40, 129, 49, 49, 49, 49, 49, 49, 3, 1, 3] 150 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]) total number of confs: 385 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 755) grep: /scratch/xiaobo/369383/xbb-8058088.28/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](CO)Cc1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635900467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635900467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001635900467 none O=C(NC[C@H](CO)Cc1ccc(C(F)(F)F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 14, 38, 35, 41, 36, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 40, 40, 123, 49, 49, 49, 49, 49, 49, 3, 1, 3] 150 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]) total number of confs: 365 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635900467 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900467 Building ZINC001635900468 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635900468 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/756 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635900468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635900468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001635900468 none O=C(NC[C@@H](CO)Cc1ccc(C(F)(F)F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 14, 37, 34, 41, 35, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 40, 40, 123, 49, 49, 49, 49, 49, 49, 3, 1, 3] 150 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]) total number of confs: 374 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/757 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635900468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635900468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001635900468 none O=C(NC[C@@H](CO)Cc1ccc(C(F)(F)F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 15, 40, 34, 43, 38, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 40, 41, 129, 49, 49, 49, 49, 49, 49, 3, 1, 3] 150 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]) total number of confs: 385 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635900468 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 Building ZINC001635900468 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001635900468 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 756) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635900468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001635900468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001635900468 none O=C(NC[C@@H](CO)Cc1ccc(C(F)(F)F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 14, 37, 34, 41, 35, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 40, 40, 123, 49, 49, 49, 49, 49, 49, 3, 1, 3] 150 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]) total number of confs: 374 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 757) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001635900468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001635900468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001635900468 none O=C(NC[C@@H](CO)Cc1ccc(C(F)(F)F)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 15, 40, 34, 43, 38, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 40, 41, 129, 49, 49, 49, 49, 49, 49, 3, 1, 3] 150 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]) total number of confs: 385 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001635900468 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001635900468 Building ZINC001636045596 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636045596 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/758 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001636045596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636045596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636045596 none O=C(NC1CCCCC1)OC[C@@H]1CCCN1C(=O)[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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 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: [12, 11, 12, 29, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/759 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001636045596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636045596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636045596 none O=C(NC1CCCCC1)OC[C@@H]1CCCN1C(=O)[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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 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: [14, 14, 14, 33, 50, 50, 50, 50, 50, 6, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 1, 1, 1] 50 rigid atoms, others: [51, 49, 17, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636045596 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 Building ZINC001636045596 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636045596 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 758) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(NC1CCCCC1)OC[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001636045596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636045596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636045596 none O=C(NC1CCCCC1)OC[C@@H]1CCCN1C(=O)[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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 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: [12, 11, 12, 29, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 759) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(NC1CCCCC1)OC[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001636045596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636045596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636045596 none O=C(NC1CCCCC1)OC[C@@H]1CCCN1C(=O)[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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 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: [14, 14, 14, 33, 50, 50, 50, 50, 50, 6, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 1, 1, 1] 50 rigid atoms, others: [51, 49, 17, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636045596 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045596 Building ZINC001636045597 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636045597 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/760 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001636045597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636045597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636045597 none O=C(NC1CCCCC1)OC[C@H]1CCCN1C(=O)[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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 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: [14, 14, 14, 33, 50, 50, 50, 50, 50, 6, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 1, 1, 1] 50 rigid atoms, others: [51, 49, 17, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/761 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001636045597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636045597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636045597 none O=C(NC1CCCCC1)OC[C@H]1CCCN1C(=O)[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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 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: [12, 11, 12, 29, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636045597 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 Building ZINC001636045597 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636045597 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 760) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001636045597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636045597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636045597 none O=C(NC1CCCCC1)OC[C@H]1CCCN1C(=O)[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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 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: [14, 14, 14, 33, 50, 50, 50, 50, 50, 6, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 1, 1, 1] 50 rigid atoms, others: [51, 49, 17, 50, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 761) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001636045597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636045597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636045597 none O=C(NC1CCCCC1)OC[C@H]1CCCN1C(=O)[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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 8, 1, 11, 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, 7, 4, 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: [12, 11, 12, 29, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636045597 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636045597 Building ZINC001636060493 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636060493 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/762 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/762' -> `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@@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC001636060493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636060493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001636060493 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 7, 7, 7, 15, 15, 15, 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, 52]) total number of confs: 109 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/763 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/763' -> `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@@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC001636060493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636060493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001636060493 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 9, 9, 17, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 9, 9, 9, 17, 17, 17, 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]) total number of confs: 124 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636060493 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 Building ZINC001636060493 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636060493 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 762) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC001636060493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636060493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001636060493 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 7, 7, 7, 15, 15, 15, 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, 52]) total number of confs: 109 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 763) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC001636060493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636060493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001636060493 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 9, 9, 17, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 9, 9, 9, 17, 17, 17, 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]) total number of confs: 124 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636060493 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060493 Building ZINC001636060494 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636060494 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/764 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/764' -> `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@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC001636060494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636060494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001636060494 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 9, 9, 17, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 9, 9, 9, 17, 17, 17, 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]) total number of confs: 115 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/765 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/765' -> `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@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC001636060494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636060494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001636060494 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 8, 8, 16, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 8, 8, 8, 16, 16, 16, 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, 52]) total number of confs: 113 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636060494 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 Building ZINC001636060494 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636060494 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 764) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC001636060494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636060494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001636060494 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 9, 9, 17, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 9, 9, 9, 17, 17, 17, 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]) total number of confs: 115 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 765) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1) `ZINC001636060494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636060494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001636060494 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1nc2ccc(Cl)cc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 8, 8, 16, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 8, 8, 8, 16, 16, 16, 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, 52]) total number of confs: 113 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636060494 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636060494 Building ZINC001636064934 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636064934 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/766 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001636064934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636064934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001636064934 none C[C@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 8, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 35, 35, 35, 8, 8, 8, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/767 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001636064934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636064934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001636064934 none C[C@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 20, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 6, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 32, 32, 32, 6, 6, 6, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636064934 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 Building ZINC001636064934 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636064934 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 766) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001636064934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636064934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001636064934 none C[C@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 8, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 35, 35, 35, 8, 8, 8, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 767) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001636064934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636064934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001636064934 none C[C@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 20, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 3, 6, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 32, 32, 32, 6, 6, 6, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636064934 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064934 Building ZINC001636064935 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636064935 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/768 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001636064935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636064935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001636064935 none C[C@@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 19, 19, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3, 6, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 19, 19, 19, 34, 34, 34, 6, 6, 6, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/769 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001636064935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636064935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001636064935 none C[C@@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 8, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 35, 35, 35, 8, 8, 8, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636064935 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 Building ZINC001636064935 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636064935 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 768) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001636064935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636064935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001636064935 none C[C@@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 19, 19, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3, 6, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 19, 19, 19, 34, 34, 34, 6, 6, 6, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 769) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001636064935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636064935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001636064935 none C[C@@H](c1nc2ccc(Cl)cc2[nH]1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 8, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 35, 35, 35, 8, 8, 8, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636064935 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636064935 Building ZINC001636341845 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636341845 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/770 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/770' -> `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[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 15, 21, 21, 21, 21, 21, 21, 21, 24, 36, 36, 31, 36, 36, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 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, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/771 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/771' -> `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[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 24, 34, 34, 34, 34, 34, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 113 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/772 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/772' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 15, 21, 21, 21, 21, 21, 21, 21, 24, 36, 36, 31, 36, 36, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 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, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/773 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/773' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 24, 34, 34, 34, 34, 34, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 113 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636341845 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 Building ZINC001636341845 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636341845 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 770) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 15, 21, 21, 21, 21, 21, 21, 21, 24, 36, 36, 31, 36, 36, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 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, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 771) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 24, 34, 34, 34, 34, 34, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 113 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 772) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 15, 21, 21, 21, 21, 21, 21, 21, 24, 36, 36, 31, 36, 36, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 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, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 773) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 24, 34, 34, 34, 34, 34, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 113 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636341845 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 Building ZINC001636341845 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636341845 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 770) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 15, 21, 21, 21, 21, 21, 21, 21, 24, 36, 36, 31, 36, 36, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 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, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 771) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 24, 34, 34, 34, 34, 34, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 113 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 772) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 15, 21, 21, 21, 21, 21, 21, 21, 24, 36, 36, 31, 36, 36, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 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, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 773) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 24, 34, 34, 34, 34, 34, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 113 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636341845 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 Building ZINC001636341845 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636341845 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 770) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 15, 21, 21, 21, 21, 21, 21, 21, 24, 36, 36, 31, 36, 36, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 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, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 771) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 24, 34, 34, 34, 34, 34, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 113 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 772) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 15, 21, 21, 21, 21, 21, 21, 21, 24, 36, 36, 31, 36, 36, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 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, 62, 63, 64]) total number of confs: 138 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 773) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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[C@H]1CCCCN1Cc1ccccc1) `ZINC001636341845.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636341845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001636341845 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H]1CCCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 24, 34, 34, 34, 34, 34, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 24, 24, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 113 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636341845 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636341845 Building ZINC001636422382 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636422382 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/774 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCN(CCc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001636422382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636422382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001636422382 none CC(C)(C)OC(=O)NCCN(CCc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 31, 42, 13, 11, 5, 4, 5, 9, 9, 9, 9, 9, 9, 9, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 13, 13, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/775 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCN(CCc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001636422382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636422382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001636422382 none CC(C)(C)OC(=O)NCCN(CCc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 40, 13, 11, 5, 4, 5, 9, 9, 9, 9, 9, 9, 9, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 45, 45, 45, 45, 45, 45, 45, 45, 45, 29, 13, 13, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636422382 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 Building ZINC001636422382 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636422382 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 774) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NCCN(CCc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001636422382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636422382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001636422382 none CC(C)(C)OC(=O)NCCN(CCc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 31, 42, 13, 11, 5, 4, 5, 9, 9, 9, 9, 9, 9, 9, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 13, 13, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 775) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NCCN(CCc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001636422382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636422382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001636422382 none CC(C)(C)OC(=O)NCCN(CCc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Cl)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.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 40, 13, 11, 5, 4, 5, 9, 9, 9, 9, 9, 9, 9, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 45, 45, 45, 45, 45, 45, 45, 45, 45, 29, 13, 13, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636422382 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636422382 Building ZINC001636519664 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636519664 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/776 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(I)c(Cl)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636519664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636519664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001636519664 none O=C(Nc1ccc(I)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', 'I', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 16, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 28, 28, 20, 28, 28, 28, 28, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 28, 28, 28, 8, 8, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/777 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(I)c(Cl)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636519664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636519664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001636519664 none O=C(Nc1ccc(I)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', 'I', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 16, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 28, 28, 18, 28, 28, 28, 28, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 28, 28, 28, 8, 8, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636519664 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 Building ZINC001636519664 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636519664 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 776) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(Nc1ccc(I)c(Cl)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636519664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636519664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001636519664 none O=C(Nc1ccc(I)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', 'I', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 16, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 28, 28, 20, 28, 28, 28, 28, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 28, 28, 28, 8, 8, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 777) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(Nc1ccc(I)c(Cl)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636519664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636519664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001636519664 none O=C(Nc1ccc(I)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', 'I', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 16, 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, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 28, 28, 18, 28, 28, 28, 28, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 28, 28, 28, 8, 8, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636519664 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636519664 Building ZINC001636560758 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636560758 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/778 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 46, 46, 19, 46, 46, 46, 7, 7, 7, 7, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 7, 7, 7, 7, 46, 46, 46, 46, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/779 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 36, 36, 29, 36, 36, 36, 6, 6, 6, 6, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 6, 6, 6, 6, 36, 36, 36, 36, 6, 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]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/780 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/780' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 46, 46, 19, 46, 46, 46, 7, 7, 7, 7, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 7, 7, 7, 7, 46, 46, 46, 46, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/781 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/781' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 36, 36, 29, 36, 36, 36, 6, 6, 6, 6, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 6, 6, 6, 6, 36, 36, 36, 36, 6, 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]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636560758 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 Building ZINC001636560758 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636560758 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 778) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 46, 46, 19, 46, 46, 46, 7, 7, 7, 7, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 7, 7, 7, 7, 46, 46, 46, 46, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 779) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 36, 36, 29, 36, 36, 36, 6, 6, 6, 6, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 6, 6, 6, 6, 36, 36, 36, 36, 6, 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]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 780) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 46, 46, 19, 46, 46, 46, 7, 7, 7, 7, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 7, 7, 7, 7, 46, 46, 46, 46, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 781) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 36, 36, 29, 36, 36, 36, 6, 6, 6, 6, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 6, 6, 6, 6, 36, 36, 36, 36, 6, 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]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636560758 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 Building ZINC001636560758 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636560758 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 778) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 46, 46, 19, 46, 46, 46, 7, 7, 7, 7, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 7, 7, 7, 7, 46, 46, 46, 46, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 779) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 36, 36, 29, 36, 36, 36, 6, 6, 6, 6, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 6, 6, 6, 6, 36, 36, 36, 36, 6, 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]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 780) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 46, 46, 19, 46, 46, 46, 7, 7, 7, 7, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 7, 7, 7, 7, 46, 46, 46, 46, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 781) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 36, 36, 29, 36, 36, 36, 6, 6, 6, 6, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 6, 6, 6, 6, 36, 36, 36, 36, 6, 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]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636560758 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 Building ZINC001636560758 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636560758 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 778) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 46, 46, 19, 46, 46, 46, 7, 7, 7, 7, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 7, 7, 7, 7, 46, 46, 46, 46, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 779) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 36, 36, 29, 36, 36, 36, 6, 6, 6, 6, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 6, 6, 6, 6, 36, 36, 36, 36, 6, 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]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 780) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 46, 46, 19, 46, 46, 46, 7, 7, 7, 7, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 7, 7, 7, 7, 46, 46, 46, 46, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 166 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 781) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@@H]1C) `ZINC001636560758.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636560758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560758 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 36, 36, 29, 36, 36, 36, 6, 6, 6, 6, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 6, 6, 6, 6, 36, 36, 36, 36, 6, 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]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636560758 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560758 Building ZINC001636560759 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636560759 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/782 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 6, 7, 7, 7, 7, 36, 36, 20, 36, 36, 36, 7, 7, 7, 7, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 7, 7, 7, 7, 36, 36, 36, 36, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 128 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/783 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 7, 8, 8, 8, 8, 41, 41, 29, 41, 41, 41, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 8, 8, 8, 8, 41, 41, 41, 41, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/784 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/784' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 6, 7, 7, 7, 7, 36, 36, 20, 36, 36, 36, 7, 7, 7, 7, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 7, 7, 7, 7, 36, 36, 36, 36, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 128 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/785 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/785' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 7, 8, 8, 8, 8, 41, 41, 29, 41, 41, 41, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 8, 8, 8, 8, 41, 41, 41, 41, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636560759 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 Building ZINC001636560759 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636560759 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 782) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 6, 7, 7, 7, 7, 36, 36, 20, 36, 36, 36, 7, 7, 7, 7, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 7, 7, 7, 7, 36, 36, 36, 36, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 128 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 783) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 7, 8, 8, 8, 8, 41, 41, 29, 41, 41, 41, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 8, 8, 8, 8, 41, 41, 41, 41, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 784) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 6, 7, 7, 7, 7, 36, 36, 20, 36, 36, 36, 7, 7, 7, 7, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 7, 7, 7, 7, 36, 36, 36, 36, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 128 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 785) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 7, 8, 8, 8, 8, 41, 41, 29, 41, 41, 41, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 8, 8, 8, 8, 41, 41, 41, 41, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636560759 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 Building ZINC001636560759 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636560759 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 782) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 6, 7, 7, 7, 7, 36, 36, 20, 36, 36, 36, 7, 7, 7, 7, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 7, 7, 7, 7, 36, 36, 36, 36, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 128 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 783) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 7, 8, 8, 8, 8, 41, 41, 29, 41, 41, 41, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 8, 8, 8, 8, 41, 41, 41, 41, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 784) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 6, 7, 7, 7, 7, 36, 36, 20, 36, 36, 36, 7, 7, 7, 7, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 7, 7, 7, 7, 36, 36, 36, 36, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 128 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 785) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 7, 8, 8, 8, 8, 41, 41, 29, 41, 41, 41, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 8, 8, 8, 8, 41, 41, 41, 41, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636560759 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 Building ZINC001636560759 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001636560759 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 782) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 6, 7, 7, 7, 7, 36, 36, 20, 36, 36, 36, 7, 7, 7, 7, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 7, 7, 7, 7, 36, 36, 36, 36, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 128 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 783) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 7, 8, 8, 8, 8, 41, 41, 29, 41, 41, 41, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 8, 8, 8, 8, 41, 41, 41, 41, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 784) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 6, 7, 7, 7, 7, 36, 36, 20, 36, 36, 36, 7, 7, 7, 7, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 7, 7, 7, 7, 36, 36, 36, 36, 7, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 128 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 785) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[C@H]1C) `ZINC001636560759.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001636560759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636560759 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cccc(Cl)c2)C[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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 7, 8, 8, 8, 8, 41, 41, 29, 41, 41, 41, 8, 8, 8, 8, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 8, 8, 8, 8, 41, 41, 41, 41, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636560759 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636560759 Building ZINC001636613527 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636613527 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/786 `/scratch/xiaobo/369383/xbb-8058088.28/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)N1CC(c2cccc(C(F)(F)F)c2)C1) `ZINC001636613527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636613527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636613527 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 2, 18, 18, 2, 18, 18, 18, 18, 18, 18, 2, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 3, 2, 2, 2, 18, 18, 2, 18, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/787 `/scratch/xiaobo/369383/xbb-8058088.28/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)N1CC(c2cccc(C(F)(F)F)c2)C1) `ZINC001636613527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636613527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636613527 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 2, 19, 19, 2, 19, 19, 19, 19, 19, 19, 2, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 2, 2, 19, 19, 2, 19, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636613527 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 Building ZINC001636613527 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636613527 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 786) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)N1CC(c2cccc(C(F)(F)F)c2)C1) `ZINC001636613527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636613527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636613527 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 2, 18, 18, 2, 18, 18, 18, 18, 18, 18, 2, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 3, 2, 2, 2, 18, 18, 2, 18, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 787) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)N1CC(c2cccc(C(F)(F)F)c2)C1) `ZINC001636613527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636613527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001636613527 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(c2cccc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 2, 2, 2, 19, 19, 2, 19, 19, 19, 19, 19, 19, 2, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 2, 2, 19, 19, 2, 19, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636613527 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636613527 Building ZINC001636790364 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636790364 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/788 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C1) `ZINC001636790364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636790364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001636790364 none CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 23, 24, 23, 23, 23, 23, 23, 23, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 23, 23, 23, 23, 23, 23, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/789 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C1) `ZINC001636790364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636790364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001636790364 none CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 25, 23, 23, 23, 23, 23, 23, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 23, 23, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 23, 23, 23, 23, 23, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636790364 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 Building ZINC001636790364 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636790364 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 788) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C1) `ZINC001636790364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636790364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001636790364 none CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 23, 24, 23, 23, 23, 23, 23, 23, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 23, 23, 23, 23, 23, 23, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 789) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C1) `ZINC001636790364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636790364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001636790364 none CC(C)(C)OC(=O)N1CCOc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 25, 23, 23, 23, 23, 23, 23, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 12, 23, 23, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 23, 23, 23, 23, 23, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636790364 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636790364 Building ZINC001636866217 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636866217 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/790 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1) `ZINC001636866217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636866217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001636866217 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 7, 18, 18, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 7, 13, 13, 13, 19, 18, 18, 18, 18, 18, 18, 18, 4, 7, 7, 7, 7, 13, 13, 13, 13, 19, 19, 19, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/791 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1) `ZINC001636866217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636866217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001636866217 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 17, 17, 8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 13, 13, 8, 13, 13, 13, 19, 17, 17, 17, 17, 17, 17, 17, 4, 7, 7, 7, 7, 13, 13, 13, 13, 19, 19, 19, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636866217 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 Building ZINC001636866217 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636866217 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 790) grep: /scratch/xiaobo/369383/xbb-8058088.28/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@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1) `ZINC001636866217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636866217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001636866217 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 7, 18, 18, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 7, 13, 13, 13, 19, 18, 18, 18, 18, 18, 18, 18, 4, 7, 7, 7, 7, 13, 13, 13, 13, 19, 19, 19, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 791) grep: /scratch/xiaobo/369383/xbb-8058088.28/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@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1) `ZINC001636866217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636866217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001636866217 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 17, 17, 8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 13, 13, 8, 13, 13, 13, 19, 17, 17, 17, 17, 17, 17, 17, 4, 7, 7, 7, 7, 13, 13, 13, 13, 19, 19, 19, 17, 17] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636866217 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866217 Building ZINC001636866218 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636866218 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/792 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1) `ZINC001636866218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636866218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001636866218 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 8, 18, 18, 8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 13, 13, 8, 13, 13, 13, 18, 18, 18, 18, 18, 18, 18, 18, 4, 7, 7, 7, 7, 13, 13, 13, 13, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/793 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1) `ZINC001636866218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636866218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001636866218 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 12, 7, 18, 18, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 7, 13, 13, 13, 19, 18, 18, 18, 18, 18, 18, 18, 4, 7, 7, 7, 7, 13, 13, 13, 13, 19, 19, 19, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636866218 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 Building ZINC001636866218 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636866218 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 792) grep: /scratch/xiaobo/369383/xbb-8058088.28/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@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1) `ZINC001636866218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636866218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001636866218 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 8, 18, 18, 8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 13, 13, 8, 13, 13, 13, 18, 18, 18, 18, 18, 18, 18, 18, 4, 7, 7, 7, 7, 13, 13, 13, 13, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 793) grep: /scratch/xiaobo/369383/xbb-8058088.28/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@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1) `ZINC001636866218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636866218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001636866218 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 12, 7, 18, 18, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 7, 13, 13, 13, 19, 18, 18, 18, 18, 18, 18, 18, 4, 7, 7, 7, 7, 13, 13, 13, 13, 19, 19, 19, 18, 18] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636866218 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636866218 Building ZINC001636872729 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636872729 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/794 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1(CNC(=O)OC(C)(C)C)CCCCC1) `ZINC001636872729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636872729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001636872729 none CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 14, 21, 34, 34, 40, 40, 40, 40, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 14, 14, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 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, 57, 58, 59, 60]) total number of confs: 149 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/795 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1(CNC(=O)OC(C)(C)C)CCCCC1) `ZINC001636872729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636872729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001636872729 none CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 13, 22, 32, 32, 40, 40, 40, 40, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 13, 13, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 132 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636872729 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 Building ZINC001636872729 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636872729 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 794) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1(CNC(=O)OC(C)(C)C)CCCCC1) `ZINC001636872729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636872729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001636872729 none CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 14, 21, 34, 34, 40, 40, 40, 40, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 14, 14, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 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, 57, 58, 59, 60]) total number of confs: 149 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 795) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1(CNC(=O)OC(C)(C)C)CCCCC1) `ZINC001636872729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636872729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001636872729 none CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 13, 22, 32, 32, 40, 40, 40, 40, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 13, 13, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 132 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636872729 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636872729 Building ZINC001636910802 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636910802 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/796 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ccc(F)cc2)c1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636910802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636910802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636910802 none O=C(Nc1cnn(c2ccc(F)cc2)c1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 17, 27, 27, 27, 27, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/797 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnn(c2ccc(F)cc2)c1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636910802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636910802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636910802 none O=C(Nc1cnn(c2ccc(F)cc2)c1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 17, 26, 26, 25, 25, 26, 26, 17, 17, 17, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 17, 26, 26, 26, 26, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636910802 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 Building ZINC001636910802 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636910802 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 796) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cnn(c2ccc(F)cc2)c1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636910802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636910802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636910802 none O=C(Nc1cnn(c2ccc(F)cc2)c1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 17, 27, 27, 27, 27, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 797) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(Nc1cnn(c2ccc(F)cc2)c1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001636910802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636910802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001636910802 none O=C(Nc1cnn(c2ccc(F)cc2)c1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'F', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 17, 26, 26, 25, 25, 26, 26, 17, 17, 17, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 17, 26, 26, 26, 26, 9, 9, 9, 9] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636910802 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636910802 Building ZINC001636922431 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636922431 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/798 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2) `ZINC001636922431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636922431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001636922431 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2 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', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 31, 42, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 6, 6, 6, 6, 6, 2, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/799 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2) `ZINC001636922431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636922431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001636922431 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2 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', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 31, 42, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [48, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/369383/xbb-8058088.28/working/building/ZINC001636922431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636922431 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431 Building ZINC001636922431 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001636922431 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 798) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2) `ZINC001636922431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001636922431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001636922431 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2 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', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 31, 42, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 6, 6, 6, 6, 6, 2, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 799) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2) `ZINC001636922431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001636922431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001636922431 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2 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', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 31, 42, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [48, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/369383/xbb-8058088.28/working/building/ZINC001636922431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001636922431 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001636922431 Building ZINC001637023961 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637023961 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/800 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2cccc(C(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001637023961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637023961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637023961 none O=C(N1CC(Cc2cccc(C(F)(F)F)c2)C1)[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', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 7, 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, 3, 9, 9, 9, 23, 36, 36, 35, 36, 36, 36, 36, 36, 36, 9, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 23, 23, 36, 36, 36, 36, 9, 9, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/801 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2cccc(C(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001637023961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637023961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637023961 none O=C(N1CC(Cc2cccc(C(F)(F)F)c2)C1)[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', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 7, 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: [1, 1, 2, 8, 8, 8, 20, 35, 35, 32, 35, 35, 35, 35, 35, 35, 8, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 20, 20, 35, 35, 35, 35, 8, 8, 3, 3] 50 rigid atoms, others: [0, 1, 18, 19, 17] set([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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637023961 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 Building ZINC001637023961 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637023961 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 800) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CC(Cc2cccc(C(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001637023961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637023961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637023961 none O=C(N1CC(Cc2cccc(C(F)(F)F)c2)C1)[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', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 7, 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, 3, 9, 9, 9, 23, 36, 36, 35, 36, 36, 36, 36, 36, 36, 9, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 23, 23, 36, 36, 36, 36, 9, 9, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 801) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CC(Cc2cccc(C(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001637023961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637023961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637023961 none O=C(N1CC(Cc2cccc(C(F)(F)F)c2)C1)[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', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 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, 7, 7, 7, 7, 7, 7, 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: [1, 1, 2, 8, 8, 8, 20, 35, 35, 32, 35, 35, 35, 35, 35, 35, 8, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 20, 20, 35, 35, 35, 35, 8, 8, 3, 3] 50 rigid atoms, others: [0, 1, 18, 19, 17] set([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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637023961 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637023961 Building ZINC001637119965 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637119965 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/802 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/802' -> `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])c1c[nH]c2cc(F)ccc21) `ZINC001637119965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637119965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001637119965 none O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[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', '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.2', 'C.2', 'N.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, 1, 1, 1, 1, 1, 11, 12, 5, 1, 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 9, 14, 30, 30, 30, 34, 34, 34, 34, 34, 34, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 14, 14, 34, 34, 34, 34, 34, 34, 34, 14, 14, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/803 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/803' -> `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])c1c[nH]c2cc(F)ccc21) `ZINC001637119965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637119965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001637119965 none O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[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', '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.2', 'C.2', 'N.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, 1, 1, 1, 1, 1, 11, 12, 5, 1, 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 9, 12, 30, 30, 30, 34, 34, 34, 34, 34, 34, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 14, 14, 34, 34, 34, 34, 34, 34, 34, 14, 14, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637119965 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 Building ZINC001637119965 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637119965 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 802) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637119965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637119965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001637119965 none O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[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', '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.2', 'C.2', 'N.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, 1, 1, 1, 1, 1, 11, 12, 5, 1, 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 9, 14, 30, 30, 30, 34, 34, 34, 34, 34, 34, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 14, 14, 34, 34, 34, 34, 34, 34, 34, 14, 14, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 803) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637119965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637119965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001637119965 none O=C(NCc1ccc(C(=O)OCc2ccccc2)cc1)[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', '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.2', 'C.2', 'N.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, 1, 1, 1, 1, 1, 11, 12, 5, 1, 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, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 9, 12, 30, 30, 30, 34, 34, 34, 34, 34, 34, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 14, 14, 34, 34, 34, 34, 34, 34, 34, 14, 14, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637119965 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637119965 Building ZINC001637252592 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637252592 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/804 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001637252592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637252592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637252592 none CC(C)(C)OC(=O)N1Cc2ccccc2C[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 36, 36, 36, 36, 36, 36, 36, 36, 36, 13, 36, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 36, 13, 13, 2, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/805 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001637252592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637252592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637252592 none CC(C)(C)OC(=O)N1Cc2ccccc2C[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 14, 38, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 14, 14, 2, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637252592 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 Building ZINC001637252592 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637252592 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 804) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1Cc2ccccc2C[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001637252592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637252592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637252592 none CC(C)(C)OC(=O)N1Cc2ccccc2C[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 36, 36, 36, 36, 36, 36, 36, 36, 36, 13, 36, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 36, 13, 13, 2, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 805) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1Cc2ccccc2C[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001637252592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637252592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637252592 none CC(C)(C)OC(=O)N1Cc2ccccc2C[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 14, 38, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 14, 14, 2, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637252592 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252592 Building ZINC001637252593 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637252593 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/806 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001637252593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637252593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637252593 none CC(C)(C)OC(=O)N1Cc2ccccc2C[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 13, 38, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 13, 13, 2, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/807 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001637252593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637252593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637252593 none CC(C)(C)OC(=O)N1Cc2ccccc2C[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 35, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 2, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637252593 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 Building ZINC001637252593 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637252593 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 806) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1Cc2ccccc2C[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001637252593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637252593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637252593 none CC(C)(C)OC(=O)N1Cc2ccccc2C[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 13, 38, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 13, 13, 2, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 807) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1Cc2ccccc2C[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001637252593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637252593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637252593 none CC(C)(C)OC(=O)N1Cc2ccccc2C[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 35, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 2, 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]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637252593 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637252593 Building ZINC001637407291 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637407291 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/808 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/808' -> `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)NC1(CC(=O)OC(C)(C)C)CCCCC1) `ZINC001637407291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637407291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001637407291 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(CC(=O)OC(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', '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, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 9, 12, 21, 42, 42, 48, 48, 48, 48, 12, 12, 12, 12, 12, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 21, 21, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/809 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/809' -> `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)NC1(CC(=O)OC(C)(C)C)CCCCC1) `ZINC001637407291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637407291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001637407291 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(CC(=O)OC(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', '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, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 9, 12, 20, 37, 37, 46, 46, 46, 46, 12, 12, 12, 12, 12, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 20, 20, 46, 46, 46, 46, 46, 46, 46, 46, 46, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 157 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637407291 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 Building ZINC001637407291 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637407291 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 808) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(CC(=O)OC(C)(C)C)CCCCC1) `ZINC001637407291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637407291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001637407291 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(CC(=O)OC(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', '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, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 9, 12, 21, 42, 42, 48, 48, 48, 48, 12, 12, 12, 12, 12, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 21, 21, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 809) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(CC(=O)OC(C)(C)C)CCCCC1) `ZINC001637407291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637407291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001637407291 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(CC(=O)OC(C)(C)C)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', '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, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 9, 12, 20, 37, 37, 46, 46, 46, 46, 12, 12, 12, 12, 12, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 20, 20, 46, 46, 46, 46, 46, 46, 46, 46, 46, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 157 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637407291 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637407291 Building ZINC001637418428 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637418428 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/810 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637418428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418428 none C[C@@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 25, 25, 25, 25, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/811 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637418428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418428 none C[C@@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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: [5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 5, 30, 30, 30, 30, 30, 30, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 30, 30, 5, 30, 5, 5, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637418428 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 Building ZINC001637418428 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637418428 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 810) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637418428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418428 none C[C@@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 25, 25, 25, 25, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 811) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637418428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418428 none C[C@@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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: [5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 5, 30, 30, 30, 30, 30, 30, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 30, 30, 5, 30, 5, 5, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637418428 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418428 Building ZINC001637418429 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637418429 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/812 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637418429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418429 none C[C@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 28, 28, 7, 28, 28, 28, 28, 28, 28, 7, 6, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 28, 28, 7, 28, 7, 7, 4, 4, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/813 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637418429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418429 none C[C@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 29, 29, 24, 29, 7, 7, 4, 4, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637418429 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 Building ZINC001637418429 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637418429 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 812) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637418429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418429 none C[C@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 28, 28, 7, 28, 28, 28, 28, 28, 28, 7, 6, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 28, 28, 7, 28, 7, 7, 4, 4, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 813) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637418429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418429 none C[C@H]1CO[C@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 29, 29, 24, 29, 7, 7, 4, 4, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637418429 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418429 Building ZINC001637418430 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637418430 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/814 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637418430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418430 none C[C@@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 9, 28, 28, 28, 28, 28, 28, 6, 5, 3, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 28, 28, 19, 28, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/815 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637418430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418430 none C[C@@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 7, 27, 27, 27, 27, 27, 27, 6, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 27, 27, 6, 27, 6, 6, 4, 4, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637418430 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 Building ZINC001637418430 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637418430 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 814) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637418430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418430 none C[C@@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 9, 28, 28, 28, 28, 28, 28, 6, 5, 3, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 28, 28, 19, 28, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 815) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637418430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418430 none C[C@@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 7, 27, 27, 27, 27, 27, 27, 6, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 27, 27, 6, 27, 6, 6, 4, 4, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637418430 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418430 Building ZINC001637418431 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637418431 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/816 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637418431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418431 none C[C@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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: [5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 7, 33, 33, 33, 33, 33, 33, 5, 3, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 33, 33, 7, 33, 5, 5, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/817 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637418431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418431 none C[C@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 4, 4, 4, 26, 26, 6, 26, 26, 26, 26, 26, 26, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 26, 26, 6, 26, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637418431 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 Building ZINC001637418431 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637418431 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 816) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637418431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418431 none C[C@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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: [5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 7, 33, 33, 33, 33, 33, 33, 5, 3, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 33, 33, 7, 33, 5, 5, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 817) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001637418431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637418431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001637418431 none C[C@H]1CO[C@@H](c2cccc(C(F)(F)F)c2)CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 4, 4, 4, 26, 26, 6, 26, 26, 26, 26, 26, 26, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 26, 26, 6, 26, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637418431 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637418431 Building ZINC001637605876 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637605876 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/818 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](Oc2cncc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637605876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637605876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001637605876 none O=C(N1CC[C@H](Oc2cncc(Br)c2)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', 'O.3', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 8, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 22, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 5, 5, 5, 50, 50, 50, 5, 5, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/819 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](Oc2cncc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637605876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637605876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001637605876 none O=C(N1CC[C@H](Oc2cncc(Br)c2)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', 'O.3', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 8, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 19, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 5, 5, 5, 50, 50, 50, 5, 5, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637605876 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 Building ZINC001637605876 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637605876 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 818) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](Oc2cncc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637605876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637605876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001637605876 none O=C(N1CC[C@H](Oc2cncc(Br)c2)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', 'O.3', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 8, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 22, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 5, 5, 5, 50, 50, 50, 5, 5, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 819) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](Oc2cncc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637605876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637605876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001637605876 none O=C(N1CC[C@H](Oc2cncc(Br)c2)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', 'O.3', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 8, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 19, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 5, 5, 5, 50, 50, 50, 5, 5, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637605876 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605876 Building ZINC001637605877 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637605877 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/820 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](Oc2cncc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637605877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637605877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001637605877 none O=C(N1CC[C@@H](Oc2cncc(Br)c2)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', 'O.3', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 8, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 20, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 5, 5, 5, 50, 50, 50, 5, 5, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/821 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](Oc2cncc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637605877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637605877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001637605877 none O=C(N1CC[C@@H](Oc2cncc(Br)c2)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', 'O.3', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 8, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 20, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 5, 5, 5, 50, 50, 50, 5, 5, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637605877 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 Building ZINC001637605877 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637605877 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 820) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](Oc2cncc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637605877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637605877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001637605877 none O=C(N1CC[C@@H](Oc2cncc(Br)c2)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', 'O.3', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 8, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 20, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 5, 5, 5, 50, 50, 50, 5, 5, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 821) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](Oc2cncc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637605877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637605877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001637605877 none O=C(N1CC[C@@H](Oc2cncc(Br)c2)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', 'O.3', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 1, 1, 8, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 20, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 5, 5, 5, 50, 50, 50, 5, 5, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637605877 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637605877 Building ZINC001637689641 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637689641 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/822 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)OC(C)(C)C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1) `ZINC001637689641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637689641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001637689641 none CN(C(=O)OC(C)(C)C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 23, 31, 31, 31, 31, 31, 31, 13, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 17, 24, 24, 24, 24, 24, 24, 23, 23, 23, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 5, 5, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/823 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)OC(C)(C)C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1) `ZINC001637689641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637689641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001637689641 none CN(C(=O)OC(C)(C)C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 26, 32, 32, 32, 32, 32, 32, 14, 23, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 23, 29, 29, 29, 29, 29, 29, 26, 26, 26, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 2, 6, 6, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637689641 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 Building ZINC001637689641 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637689641 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 822) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C(=O)OC(C)(C)C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1) `ZINC001637689641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637689641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001637689641 none CN(C(=O)OC(C)(C)C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 23, 31, 31, 31, 31, 31, 31, 13, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 17, 24, 24, 24, 24, 24, 24, 23, 23, 23, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 5, 5, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 823) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C(=O)OC(C)(C)C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1) `ZINC001637689641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637689641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001637689641 none CN(C(=O)OC(C)(C)C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 26, 32, 32, 32, 32, 32, 32, 14, 23, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 23, 29, 29, 29, 29, 29, 29, 26, 26, 26, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 2, 6, 6, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637689641 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689641 Building ZINC001637689642 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637689642 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/824 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)OC(C)(C)C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1) `ZINC001637689642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637689642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001637689642 none CN(C(=O)OC(C)(C)C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 26, 33, 33, 34, 34, 34, 34, 14, 23, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 23, 29, 29, 29, 29, 29, 29, 26, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 2, 5, 5, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/825 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)OC(C)(C)C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1) `ZINC001637689642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637689642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001637689642 none CN(C(=O)OC(C)(C)C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 22, 30, 30, 31, 31, 31, 31, 11, 16, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 16, 23, 23, 23, 23, 23, 23, 22, 22, 22, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11, 11, 2, 5, 5, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637689642 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 Building ZINC001637689642 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637689642 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 824) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C(=O)OC(C)(C)C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1) `ZINC001637689642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637689642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001637689642 none CN(C(=O)OC(C)(C)C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 26, 33, 33, 34, 34, 34, 34, 14, 23, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 23, 29, 29, 29, 29, 29, 29, 26, 26, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 2, 5, 5, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 825) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C(=O)OC(C)(C)C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1) `ZINC001637689642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637689642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001637689642 none CN(C(=O)OC(C)(C)C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 22, 30, 30, 31, 31, 31, 31, 11, 16, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 16, 23, 23, 23, 23, 23, 23, 22, 22, 22, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11, 11, 2, 5, 5, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637689642 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637689642 Building ZINC001637777668 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637777668 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/826 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC([C@@H](O)c2cc(F)ccc2F)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637777668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637777668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001637777668 none O=C(N1CCC([C@@H](O)c2cc(F)ccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 7, 12, 1, 1, 1, 15, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 8, 8, 8, 8, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 75, 45, 45, 45, 8, 8, 8, 8, 3, 1, 3] 150 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: 206 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/827 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC([C@@H](O)c2cc(F)ccc2F)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637777668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637777668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001637777668 none O=C(N1CCC([C@@H](O)c2cc(F)ccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 7, 12, 1, 1, 1, 15, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 9, 9, 9, 9, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 96, 49, 49, 49, 9, 9, 9, 9, 3, 1, 3] 150 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: 238 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637777668 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 Building ZINC001637777668 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637777668 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 826) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC([C@@H](O)c2cc(F)ccc2F)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637777668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637777668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001637777668 none O=C(N1CCC([C@@H](O)c2cc(F)ccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 7, 12, 1, 1, 1, 15, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 8, 8, 8, 8, 25, 25, 25, 45, 45, 45, 45, 45, 45, 45, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 75, 45, 45, 45, 8, 8, 8, 8, 3, 1, 3] 150 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: 206 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 827) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC([C@@H](O)c2cc(F)ccc2F)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637777668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637777668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001637777668 none O=C(N1CCC([C@@H](O)c2cc(F)ccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 7, 12, 1, 1, 1, 15, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 9, 9, 9, 9, 32, 32, 32, 49, 49, 49, 49, 49, 49, 49, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 96, 49, 49, 49, 9, 9, 9, 9, 3, 1, 3] 150 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: 238 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637777668 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777668 Building ZINC001637777669 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637777669 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/828 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC([C@H](O)c2cc(F)ccc2F)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637777669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637777669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001637777669 none O=C(N1CCC([C@H](O)c2cc(F)ccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 7, 12, 1, 1, 1, 15, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 8, 8, 8, 8, 26, 26, 26, 44, 44, 44, 44, 44, 44, 44, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 78, 44, 44, 44, 8, 8, 8, 8, 3, 1, 3] 150 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: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/829 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC([C@H](O)c2cc(F)ccc2F)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637777669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637777669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001637777669 none O=C(N1CCC([C@H](O)c2cc(F)ccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 7, 12, 1, 1, 1, 15, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 9, 9, 9, 9, 27, 27, 27, 47, 47, 47, 47, 47, 47, 47, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 81, 47, 47, 47, 9, 9, 9, 9, 3, 1, 3] 150 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: 213 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637777669 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 Building ZINC001637777669 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637777669 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 828) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC([C@H](O)c2cc(F)ccc2F)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637777669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637777669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001637777669 none O=C(N1CCC([C@H](O)c2cc(F)ccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 7, 12, 1, 1, 1, 15, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 8, 8, 8, 8, 26, 26, 26, 44, 44, 44, 44, 44, 44, 44, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 78, 44, 44, 44, 8, 8, 8, 8, 3, 1, 3] 150 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: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 829) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC([C@H](O)c2cc(F)ccc2F)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637777669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637777669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001637777669 none O=C(N1CCC([C@H](O)c2cc(F)ccc2F)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 7, 12, 1, 1, 1, 15, 1, 1, 1, 15, 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] 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 9, 9, 9, 9, 27, 27, 27, 47, 47, 47, 47, 47, 47, 47, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 81, 47, 47, 47, 9, 9, 9, 9, 3, 1, 3] 150 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: 213 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637777669 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637777669 Building ZINC001637782547 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001637782547 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/830 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 17, 17, 17, 17, 17, 15, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 17, 17, 17, 17, 17, 17, 17, 15, 2, 2, 1, 2, 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: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/831 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 17, 17, 17, 17, 17, 15, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 17, 17, 17, 17, 17, 17, 17, 15, 2, 2, 1, 2, 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: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/832 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/832' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 18, 18, 18, 18, 18, 16, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 18, 18, 18, 18, 18, 18, 16, 2, 2, 2, 2, 18, 18] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/833 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/833' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 18, 18, 18, 18, 18, 16, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 18, 18, 18, 18, 18, 18, 16, 2, 2, 2, 2, 18, 18] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637782547 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 Building ZINC001637782547 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001637782547 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 830) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 17, 17, 17, 17, 17, 15, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 17, 17, 17, 17, 17, 17, 17, 15, 2, 2, 1, 2, 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: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 831) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 17, 17, 17, 17, 17, 15, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 17, 17, 17, 17, 17, 17, 17, 15, 2, 2, 1, 2, 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: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 832) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 18, 18, 18, 18, 18, 16, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 18, 18, 18, 18, 18, 18, 16, 2, 2, 2, 2, 18, 18] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 833) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 18, 18, 18, 18, 18, 16, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 18, 18, 18, 18, 18, 18, 16, 2, 2, 2, 2, 18, 18] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637782547 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 Building ZINC001637782547 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001637782547 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 830) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 17, 17, 17, 17, 17, 15, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 17, 17, 17, 17, 17, 17, 17, 15, 2, 2, 1, 2, 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: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 831) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 17, 17, 17, 17, 17, 15, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 17, 17, 17, 17, 17, 17, 17, 15, 2, 2, 1, 2, 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: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 832) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 18, 18, 18, 18, 18, 16, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 18, 18, 18, 18, 18, 18, 16, 2, 2, 2, 2, 18, 18] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 833) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 18, 18, 18, 18, 18, 16, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 18, 18, 18, 18, 18, 18, 16, 2, 2, 2, 2, 18, 18] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637782547 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 Building ZINC001637782547 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001637782547 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 830) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 17, 17, 17, 17, 17, 15, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 17, 17, 17, 17, 17, 17, 17, 15, 2, 2, 1, 2, 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: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 831) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations 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, 38, 50, 17, 17, 17, 17, 17, 15, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 17, 17, 17, 17, 17, 17, 17, 15, 2, 2, 1, 2, 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: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `2' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 2 (index: 832) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 18, 18, 18, 18, 18, 16, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 18, 18, 18, 18, 18, 18, 16, 2, 2, 2, 2, 18, 18] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `3' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 3 (index: 833) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2) `ZINC001637782547.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001637782547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001637782547 none CC(C)(C)OC(=O)NC1CC2(C1)CC(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C2 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', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 50, 18, 18, 18, 18, 18, 16, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 18, 18, 18, 18, 18, 18, 16, 2, 2, 2, 2, 18, 18] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637782547 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 2: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/2.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/0.* 3: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547/3.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637782547 Building ZINC001637823491 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637823491 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/834 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cnc1NCc1ccc(Cl)cc1) `ZINC001637823491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637823491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637823491 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cnc1NCc1ccc(Cl)cc1 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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 8, 8, 8, 8, 13, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 13, 31, 31, 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, 48, 49, 50, 51, 52, 53]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/835 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cnc1NCc1ccc(Cl)cc1) `ZINC001637823491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637823491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637823491 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cnc1NCc1ccc(Cl)cc1 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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 6, 8, 8, 8, 8, 14, 30, 30, 30, 30, 30, 30, 30, 8, 8, 8, 8, 2, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 14, 30, 30, 30, 30, 30, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637823491 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 Building ZINC001637823491 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637823491 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 834) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cnc1NCc1ccc(Cl)cc1) `ZINC001637823491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637823491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637823491 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cnc1NCc1ccc(Cl)cc1 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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 8, 8, 8, 8, 13, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 13, 31, 31, 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, 48, 49, 50, 51, 52, 53]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 835) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cnc1NCc1ccc(Cl)cc1) `ZINC001637823491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637823491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001637823491 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cnc1NCc1ccc(Cl)cc1 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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 8, 1, 8, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 6, 8, 8, 8, 8, 14, 30, 30, 30, 30, 30, 30, 30, 8, 8, 8, 8, 2, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 14, 30, 30, 30, 30, 30, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637823491 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637823491 Building ZINC001637861927 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637861927 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/836 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/836' -> `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(Cc2cccc(F)c2F)CC1) `ZINC001637861927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637861927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001637861927 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(Cc2cccc(F)c2F)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.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 15, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 16, 34, 34, 34, 34, 34, 34, 34, 4, 4, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 2, 4, 4, 4, 4, 4, 16, 16, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/837 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/837' -> `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(Cc2cccc(F)c2F)CC1) `ZINC001637861927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637861927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001637861927 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(Cc2cccc(F)c2F)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.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 15, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 12, 33, 33, 33, 33, 33, 33, 33, 3, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 3, 3, 3, 12, 12, 33, 33, 33, 3, 3, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637861927 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 Building ZINC001637861927 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637861927 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 836) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(Cc2cccc(F)c2F)CC1) `ZINC001637861927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637861927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001637861927 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(Cc2cccc(F)c2F)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.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 15, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 16, 34, 34, 34, 34, 34, 34, 34, 4, 4, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 2, 4, 4, 4, 4, 4, 16, 16, 34, 34, 34, 4, 4, 4, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 837) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(Cc2cccc(F)c2F)CC1) `ZINC001637861927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637861927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001637861927 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(Cc2cccc(F)c2F)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.ar', 'F', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 15, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 12, 33, 33, 33, 33, 33, 33, 33, 3, 3, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 3, 3, 3, 3, 12, 12, 33, 33, 33, 3, 3, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637861927 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637861927 Building ZINC001637897950 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637897950 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/838 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCO)Cc1cc(Br)ccc1F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637897950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637897950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001637897950 none O=C(N(CCO)Cc1cc(Br)ccc1F)[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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 14, 16, 7, 17, 34, 34, 34, 29, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 16, 16, 48, 17, 17, 34, 34, 34, 3, 1, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 213 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/839 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCO)Cc1cc(Br)ccc1F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637897950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637897950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001637897950 none O=C(N(CCO)Cc1cc(Br)ccc1F)[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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 17, 7, 19, 34, 34, 34, 29, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 17, 17, 51, 19, 19, 34, 34, 34, 3, 1, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 222 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637897950 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 Building ZINC001637897950 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001637897950 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 838) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N(CCO)Cc1cc(Br)ccc1F)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637897950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001637897950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001637897950 none O=C(N(CCO)Cc1cc(Br)ccc1F)[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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 14, 16, 7, 17, 34, 34, 34, 29, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 16, 16, 48, 17, 17, 34, 34, 34, 3, 1, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 213 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 839) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N(CCO)Cc1cc(Br)ccc1F)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001637897950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001637897950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001637897950 none O=C(N(CCO)Cc1cc(Br)ccc1F)[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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 17, 1, 1, 1, 15, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 17, 7, 19, 34, 34, 34, 29, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 17, 17, 51, 19, 19, 34, 34, 34, 3, 1, 3] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 222 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001637897950 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001637897950 Building ZINC001638002252 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638002252 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/840 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001638002252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638002252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638002252 none CC(C)c1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 10, 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, 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] 0 hydrogens 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, 30, 21, 10, 10, 10, 10, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 21, 21, 10, 10, 10, 10, 2, 2, 10, 10, 10, 10, 30, 30] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/841 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001638002252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638002252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638002252 none CC(C)c1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 10, 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, 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] 0 hydrogens 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, 19, 8, 8, 8, 8, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 19, 19, 8, 8, 8, 8, 3, 3, 8, 8, 8, 8, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638002252 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 Building ZINC001638002252 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638002252 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 840) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)c1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001638002252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638002252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638002252 none CC(C)c1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 10, 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, 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] 0 hydrogens 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, 30, 21, 10, 10, 10, 10, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 21, 21, 10, 10, 10, 10, 2, 2, 10, 10, 10, 10, 30, 30] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 841) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)c1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001638002252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638002252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001638002252 none CC(C)c1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 10, 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, 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] 0 hydrogens 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, 19, 8, 8, 8, 8, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 19, 19, 8, 8, 8, 8, 3, 3, 8, 8, 8, 8, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638002252 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638002252 Building ZINC001638124956 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638124956 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/842 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccccc1) `ZINC001638124956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638124956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001638124956 none CCOC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 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: [33, 29, 29, 6, 29, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 15, 15, 6, 15, 15, 33, 33, 33, 33, 33, 3, 4, 4, 4, 4, 15, 15, 6, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/843 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccccc1) `ZINC001638124956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638124956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001638124956 none CCOC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 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: [33, 29, 29, 6, 29, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 15, 15, 6, 15, 15, 33, 33, 33, 33, 33, 3, 4, 4, 4, 4, 15, 15, 11, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638124956 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 Building ZINC001638124956 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638124956 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 842) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccccc1) `ZINC001638124956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638124956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001638124956 none CCOC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 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: [33, 29, 29, 6, 29, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 15, 15, 6, 15, 15, 33, 33, 33, 33, 33, 3, 4, 4, 4, 4, 15, 15, 6, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 843) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCOC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccccc1) `ZINC001638124956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638124956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001638124956 none CCOC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)nc1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 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: [33, 29, 29, 6, 29, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 15, 15, 6, 15, 15, 33, 33, 33, 33, 33, 3, 4, 4, 4, 4, 15, 15, 11, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638124956 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638124956 Building ZINC001638136756 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638136756 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/844 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1) `ZINC001638136756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638136756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001638136756 none CC(C)(C)OC(=O)N1CC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 28, 16, 16, 16, 16, 16, 16, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 16, 2, 1, 2, 16, 16, 16, 16] 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/845 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1) `ZINC001638136756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638136756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001638136756 none CC(C)(C)OC(=O)N1CC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 29, 16, 16, 16, 16, 16, 16, 2, 1, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 16, 2, 1, 2, 16, 16, 16, 16] 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638136756 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 Building ZINC001638136756 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638136756 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 844) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1) `ZINC001638136756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638136756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001638136756 none CC(C)(C)OC(=O)N1CC[C@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 28, 16, 16, 16, 16, 16, 16, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 16, 2, 1, 2, 16, 16, 16, 16] 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 845) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1) `ZINC001638136756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638136756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001638136756 none CC(C)(C)OC(=O)N1CC[C@]2(CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 29, 16, 16, 16, 16, 16, 16, 2, 1, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 16, 2, 1, 2, 16, 16, 16, 16] 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638136756 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136756 Building ZINC001638136757 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638136757 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/846 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1) `ZINC001638136757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638136757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001638136757 none CC(C)(C)OC(=O)N1CC[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 29, 16, 16, 16, 16, 16, 16, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 16, 2, 1, 2, 16, 16, 16, 16] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/847 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1) `ZINC001638136757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638136757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001638136757 none CC(C)(C)OC(=O)N1CC[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 15, 29, 15, 15, 15, 15, 15, 15, 2, 1, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 2, 15, 15, 15, 15] 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638136757 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 Building ZINC001638136757 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638136757 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 846) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1) `ZINC001638136757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638136757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001638136757 none CC(C)(C)OC(=O)N1CC[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 29, 16, 16, 16, 16, 16, 16, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 16, 2, 1, 2, 16, 16, 16, 16] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 847) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1) `ZINC001638136757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638136757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001638136757 none CC(C)(C)OC(=O)N1CC[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 15, 29, 15, 15, 15, 15, 15, 15, 2, 1, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 2, 15, 15, 15, 15] 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638136757 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638136757 Building ZINC001638380763 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638380763 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/848 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)c1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638380763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638380763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001638380763 none O=C(N[C@@H](CCO)c1ccccc1Br)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 9, 22, 27, 9, 17, 17, 9, 17, 17, 17, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 5, 22, 22, 27, 27, 81, 17, 17, 9, 17, 4, 2, 4] 150 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: 251 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/849 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)c1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638380763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638380763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001638380763 none O=C(N[C@@H](CCO)c1ccccc1Br)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 9, 27, 32, 9, 19, 19, 9, 19, 19, 19, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 5, 27, 27, 32, 32, 96, 19, 19, 9, 19, 4, 1, 4] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 289 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638380763 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 Building ZINC001638380763 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638380763 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 848) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)c1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638380763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638380763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001638380763 none O=C(N[C@@H](CCO)c1ccccc1Br)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 9, 22, 27, 9, 17, 17, 9, 17, 17, 17, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 5, 22, 22, 27, 27, 81, 17, 17, 9, 17, 4, 2, 4] 150 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: 251 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 849) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)c1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638380763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638380763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001638380763 none O=C(N[C@@H](CCO)c1ccccc1Br)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 9, 27, 32, 9, 19, 19, 9, 19, 19, 19, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 5, 27, 27, 32, 32, 96, 19, 19, 9, 19, 4, 1, 4] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 289 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638380763 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380763 Building ZINC001638380764 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638380764 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/850 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CCO)c1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638380764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638380764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001638380764 none O=C(N[C@H](CCO)c1ccccc1Br)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 9, 27, 32, 9, 19, 19, 9, 19, 19, 19, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 5, 27, 27, 32, 32, 96, 19, 19, 9, 19, 4, 2, 4] 150 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: 291 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/851 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CCO)c1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638380764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638380764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001638380764 none O=C(N[C@H](CCO)c1ccccc1Br)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 9, 22, 27, 9, 17, 17, 9, 17, 17, 17, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 5, 22, 22, 27, 27, 81, 17, 17, 9, 17, 4, 1, 4] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 249 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638380764 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 Building ZINC001638380764 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638380764 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 850) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@H](CCO)c1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638380764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638380764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001638380764 none O=C(N[C@H](CCO)c1ccccc1Br)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 9, 27, 32, 9, 19, 19, 9, 19, 19, 19, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 5, 27, 27, 32, 32, 96, 19, 19, 9, 19, 4, 2, 4] 150 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: 291 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 851) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N[C@H](CCO)c1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638380764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638380764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001638380764 none O=C(N[C@H](CCO)c1ccccc1Br)[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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 9, 22, 27, 9, 17, 17, 9, 17, 17, 17, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 5, 22, 22, 27, 27, 81, 17, 17, 9, 17, 4, 1, 4] 150 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 249 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638380764 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638380764 Building ZINC001638389304 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638389304 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/852 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2cccc(Br)c12)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001638389304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638389304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001638389304 none O=C(NCCc1c[nH]c2cccc(Br)c12)[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', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 24, 24, 31, 31, 31, 31, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/853 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2cccc(Br)c12)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001638389304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638389304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001638389304 none O=C(NCCc1c[nH]c2cccc(Br)c12)[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', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 24, 24, 31, 31, 31, 31, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638389304 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 Building ZINC001638389304 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638389304 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 852) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2cccc(Br)c12)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001638389304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638389304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001638389304 none O=C(NCCc1c[nH]c2cccc(Br)c12)[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', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 24, 24, 31, 31, 31, 31, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 853) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1c[nH]c2cccc(Br)c12)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001638389304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638389304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001638389304 none O=C(NCCc1c[nH]c2cccc(Br)c12)[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', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 24, 24, 31, 31, 31, 31, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638389304 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638389304 Building ZINC001638412083 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638412083 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/854 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1) `ZINC001638412083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638412083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001638412083 none CC(C)Cc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 34, 33, 33, 33, 33, 18, 11, 18, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 18, 19, 19, 33, 33, 34, 34, 34, 34, 34, 34, 34, 33, 33, 33, 33, 11, 11, 3, 7, 7, 19, 19, 19, 19, 19, 19, 33, 33] 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: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/855 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1) `ZINC001638412083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638412083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001638412083 none CC(C)Cc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 33, 37, 29, 29, 31, 31, 15, 10, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 15, 16, 16, 31, 31, 37, 37, 37, 37, 37, 37, 37, 33, 33, 31, 31, 10, 10, 3, 6, 6, 16, 16, 16, 16, 16, 16, 31, 31] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638412083 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 Building ZINC001638412083 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638412083 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 854) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)Cc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1) `ZINC001638412083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638412083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001638412083 none CC(C)Cc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 34, 33, 33, 33, 33, 18, 11, 18, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 18, 19, 19, 33, 33, 34, 34, 34, 34, 34, 34, 34, 33, 33, 33, 33, 11, 11, 3, 7, 7, 19, 19, 19, 19, 19, 19, 33, 33] 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: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 855) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)Cc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1) `ZINC001638412083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638412083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001638412083 none CC(C)Cc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 33, 37, 29, 29, 31, 31, 15, 10, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 15, 16, 16, 31, 31, 37, 37, 37, 37, 37, 37, 37, 33, 33, 31, 31, 10, 10, 3, 6, 6, 16, 16, 16, 16, 16, 16, 31, 31] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638412083 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412083 Building ZINC001638412084 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638412084 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/856 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1) `ZINC001638412084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638412084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001638412084 none CC(C)Cc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 37, 31, 31, 33, 33, 16, 11, 16, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 16, 17, 17, 33, 33, 37, 37, 37, 37, 37, 37, 37, 35, 35, 33, 33, 11, 11, 3, 6, 6, 17, 17, 17, 17, 17, 17, 33, 33] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/857 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1) `ZINC001638412084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638412084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001638412084 none CC(C)Cc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 34, 34, 18, 11, 18, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 18, 19, 19, 34, 34, 35, 35, 35, 35, 35, 35, 35, 34, 34, 34, 34, 11, 11, 2, 7, 7, 19, 19, 19, 19, 19, 19, 34, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638412084 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 Building ZINC001638412084 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638412084 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 856) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)Cc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1) `ZINC001638412084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638412084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001638412084 none CC(C)Cc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 37, 31, 31, 33, 33, 16, 11, 16, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 16, 17, 17, 33, 33, 37, 37, 37, 37, 37, 37, 37, 35, 35, 33, 33, 11, 11, 3, 6, 6, 17, 17, 17, 17, 17, 17, 33, 33] 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 857) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)Cc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1) `ZINC001638412084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638412084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001638412084 none CC(C)Cc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 34, 34, 18, 11, 18, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 18, 19, 19, 34, 34, 35, 35, 35, 35, 35, 35, 35, 34, 34, 34, 34, 11, 11, 2, 7, 7, 19, 19, 19, 19, 19, 19, 34, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638412084 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638412084 Building ZINC001638556775 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638556775 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/858 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@@H]2c2ccc(Cl)cc2)cc1Cl) `ZINC001638556775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638556775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001638556775 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@@H]2c2ccc(Cl)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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 2, 8, 8, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 11, 11, 18, 18, 8, 8, 8, 15, 15, 15, 8, 8, 11, 11, 11, 11, 11, 18, 18, 18, 18, 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/859 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@@H]2c2ccc(Cl)cc2)cc1Cl) `ZINC001638556775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638556775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001638556775 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@@H]2c2ccc(Cl)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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 6, 6, 6, 14, 14, 14, 6, 6, 8, 8, 8, 8, 8, 17, 17, 17, 17, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638556775 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 Building ZINC001638556775 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638556775 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 858) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)N2CCc3nc[nH]c3[C@@H]2c2ccc(Cl)cc2)cc1Cl) `ZINC001638556775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638556775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001638556775 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@@H]2c2ccc(Cl)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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 2, 8, 8, 1, 1, 1, 2, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 18, 18, 11, 11, 18, 18, 8, 8, 8, 15, 15, 15, 8, 8, 11, 11, 11, 11, 11, 18, 18, 18, 18, 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 859) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)N2CCc3nc[nH]c3[C@@H]2c2ccc(Cl)cc2)cc1Cl) `ZINC001638556775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638556775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001638556775 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@@H]2c2ccc(Cl)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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 6, 6, 6, 14, 14, 14, 6, 6, 8, 8, 8, 8, 8, 17, 17, 17, 17, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638556775 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556775 Building ZINC001638556776 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638556776 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/860 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@H]2c2ccc(Cl)cc2)cc1Cl) `ZINC001638556776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638556776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001638556776 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@H]2c2ccc(Cl)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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 8, 8, 17, 17, 6, 6, 6, 15, 15, 15, 6, 6, 8, 8, 8, 8, 8, 17, 17, 17, 17, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/861 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@H]2c2ccc(Cl)cc2)cc1Cl) `ZINC001638556776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638556776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001638556776 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@H]2c2ccc(Cl)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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 2, 8, 8, 1, 1, 1, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 11, 17, 17, 17, 8, 8, 8, 15, 15, 15, 8, 8, 10, 10, 10, 10, 10, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638556776 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 Building ZINC001638556776 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638556776 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 860) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@H]2c2ccc(Cl)cc2)cc1Cl) `ZINC001638556776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638556776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001638556776 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@H]2c2ccc(Cl)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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 8, 8, 17, 17, 6, 6, 6, 15, 15, 15, 6, 6, 8, 8, 8, 8, 8, 17, 17, 17, 17, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 861) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@H]2c2ccc(Cl)cc2)cc1Cl) `ZINC001638556776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638556776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001638556776 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3[C@H]2c2ccc(Cl)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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 2, 8, 8, 1, 1, 1, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 11, 17, 17, 17, 8, 8, 8, 15, 15, 15, 8, 8, 10, 10, 10, 10, 10, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638556776 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638556776 Building ZINC001638714627 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638714627 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/862 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccc(F)cc2)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1) `ZINC001638714627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638714627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001638714627 none CC(C)(C)OC(=O)N1CC[C@H](c2ccc(F)cc2)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 44, 36, 36, 36, 36, 36, 36, 37, 37, 36, 36, 37, 37, 24, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 37, 37, 37, 37, 15, 15, 3, 3, 3, 1, 3, 3, 36, 36] 50 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 156 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/863 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccc(F)cc2)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)C1) `ZINC001638714627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638714627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001638714627 none CC(C)(C)OC(=O)N1CC[C@H](c2ccc(F)cc2)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 37, 46, 37, 37, 37, 37, 37, 37, 38, 38, 37, 37, 38, 38, 24, 37, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 38, 38, 38, 38, 14, 14, 4, 3, 3, 1, 3, 3, 37, 37] 50 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 154 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638714627 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 Building ZINC001638714627 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638714627 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 862) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@H](c2ccc(F)cc2)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1) `ZINC001638714627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638714627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001638714627 none CC(C)(C)OC(=O)N1CC[C@H](c2ccc(F)cc2)[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 44, 36, 36, 36, 36, 36, 36, 37, 37, 36, 36, 37, 37, 24, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 37, 37, 37, 37, 15, 15, 3, 3, 3, 1, 3, 3, 36, 36] 50 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 156 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 863) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@H](c2ccc(F)cc2)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)C1) `ZINC001638714627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638714627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 25 is the cov attach 4 25 0 4 25 1 4 25 2 3 25 2 28 to be deleted 29 to be deleted 30 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001638714627 none CC(C)(C)OC(=O)N1CC[C@H](c2ccc(F)cc2)[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 37, 46, 37, 37, 37, 37, 37, 37, 38, 38, 37, 37, 38, 38, 24, 37, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 38, 38, 38, 38, 14, 14, 4, 3, 3, 1, 3, 3, 37, 37] 50 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 154 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638714627 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638714627 Building ZINC001638781762 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638781762 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/864 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001638781762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638781762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001638781762 none CCC(C)(C)OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 6, 6, 2, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/865 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001638781762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638781762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001638781762 none CCC(C)(C)OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 6, 6, 2, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 80 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638781762 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 Building ZINC001638781762 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638781762 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 864) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001638781762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638781762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001638781762 none CCC(C)(C)OCCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 6, 6, 2, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 865) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001638781762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638781762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001638781762 none CCC(C)(C)OCCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 15, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 6, 6, 2, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 80 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638781762 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638781762 Building ZINC001638879177 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638879177 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/866 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001638879177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638879177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879177 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 4, 4, 30, 30, 30, 30, 90] 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]) total number of confs: 171 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/867 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001638879177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638879177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879177 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 4, 4, 31, 31, 31, 31, 93] 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]) total number of confs: 174 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638879177 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 Building ZINC001638879177 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638879177 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 866) grep: /scratch/xiaobo/369383/xbb-8058088.28/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])c1ccc(Br)s1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001638879177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638879177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879177 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 4, 4, 30, 30, 30, 30, 90] 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]) total number of confs: 171 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 867) grep: /scratch/xiaobo/369383/xbb-8058088.28/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])c1ccc(Br)s1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001638879177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638879177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879177 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 4, 4, 31, 31, 31, 31, 93] 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]) total number of confs: 174 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638879177 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879177 Building ZINC001638879178 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638879178 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/868 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001638879178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638879178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879178 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 4, 4, 31, 31, 31, 31, 93] 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]) total number of confs: 178 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/869 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001638879178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638879178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879178 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 4, 4, 31, 31, 31, 31, 93] 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]) total number of confs: 173 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638879178 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 Building ZINC001638879178 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638879178 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 868) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001638879178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638879178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879178 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 4, 4, 31, 31, 31, 31, 93] 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]) total number of confs: 178 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 869) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001638879178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638879178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879178 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 4, 4, 31, 31, 31, 31, 93] 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]) total number of confs: 173 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638879178 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879178 Building ZINC001638879179 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638879179 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/870 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001638879179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638879179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879179 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 4, 4, 29, 29, 29, 29, 87] 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]) total number of confs: 164 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/871 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001638879179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638879179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879179 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 12, 6, 6, 28, 28, 28, 28, 84] 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]) total number of confs: 171 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638879179 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 Building ZINC001638879179 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638879179 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 870) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001638879179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638879179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879179 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 4, 4, 29, 29, 29, 29, 87] 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]) total number of confs: 164 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 871) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1c2cc(Cl)cc(Cl)c2C[C@H]1O) `ZINC001638879179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638879179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879179 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 12, 6, 6, 28, 28, 28, 28, 84] 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]) total number of confs: 171 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638879179 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879179 Building ZINC001638879180 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638879180 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/872 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001638879180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638879180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879180 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 11, 7, 7, 26, 26, 26, 26, 78] 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]) total number of confs: 162 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/873 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001638879180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638879180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879180 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 4, 4, 29, 29, 29, 29, 87] 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]) total number of confs: 166 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638879180 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 Building ZINC001638879180 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638879180 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 872) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001638879180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638879180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879180 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 11, 7, 7, 26, 26, 26, 26, 78] 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]) total number of confs: 162 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 873) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1c2cc(Cl)cc(Cl)c2C[C@@H]1O) `ZINC001638879180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638879180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638879180 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 11, 4, 4, 29, 29, 29, 29, 87] 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]) total number of confs: 166 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638879180 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638879180 Building ZINC001638885257 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638885257 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/874 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CC2(F)F)C1) `ZINC001638885257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638885257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638885257 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CC2(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', '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'] dock atom 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, 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, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 2, 5, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 19, 19, 10, 19, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 73 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/875 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CC2(F)F)C1) `ZINC001638885257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638885257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638885257 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CC2(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', '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'] dock atom 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, 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, 14, 14, 6, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 14, 14, 10, 14, 3, 3, 3, 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]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638885257 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 Building ZINC001638885257 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638885257 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 874) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CC2(F)F)C1) `ZINC001638885257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638885257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638885257 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CC2(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', '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'] dock atom 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, 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, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 2, 5, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 19, 19, 10, 19, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 73 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 875) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CC2(F)F)C1) `ZINC001638885257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638885257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638885257 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CC2(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', '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'] dock atom 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, 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, 14, 14, 6, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 14, 14, 10, 14, 3, 3, 3, 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]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638885257 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885257 Building ZINC001638885258 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638885258 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/876 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/876' -> `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@@]2(CC2(F)F)C1) `ZINC001638885258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638885258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638885258 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CC2(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', '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'] dock atom 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, 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, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 2, 6, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 19, 19, 19, 19, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 42 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/877 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/877' -> `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@@]2(CC2(F)F)C1) `ZINC001638885258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638885258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638885258 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CC2(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', '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'] dock atom 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, 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, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 14, 14, 14, 14, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638885258 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 Building ZINC001638885258 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638885258 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 876) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CC2(F)F)C1) `ZINC001638885258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638885258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638885258 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CC2(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', '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'] dock atom 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, 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, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 2, 6, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 19, 19, 19, 19, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 42 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 877) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CC2(F)F)C1) `ZINC001638885258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638885258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638885258 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CC2(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', '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'] dock atom 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, 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, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 14, 14, 14, 14, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638885258 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638885258 Building ZINC001638935275 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638935275 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/878 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)OC1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001638935275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638935275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001638935275 none CCC(C)(C)OC1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 46 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/879 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)OC1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001638935275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638935275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001638935275 none CCC(C)(C)OC1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638935275 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 Building ZINC001638935275 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638935275 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 878) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)OC1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001638935275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638935275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001638935275 none CCC(C)(C)OC1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 46 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 879) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCC(C)(C)OC1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1) `ZINC001638935275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638935275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001638935275 none CCC(C)(C)OC1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638935275 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638935275 Building ZINC001638958196 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638958196 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/880 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/880' -> `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(CCCC2)OC[C@@H]1C) `ZINC001638958196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638958196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638958196 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 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, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 26, 26, 3, 26, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 75 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/881 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/881' -> `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(CCCC2)OC[C@@H]1C) `ZINC001638958196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638958196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638958196 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 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, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 6, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 2, 6, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 16, 16, 12, 16, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638958196 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 Building ZINC001638958196 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638958196 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 880) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[C@@H]1C) `ZINC001638958196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638958196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638958196 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 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, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 26, 26, 3, 26, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 75 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 881) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[C@@H]1C) `ZINC001638958196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638958196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638958196 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 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, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 6, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 2, 6, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 16, 16, 12, 16, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638958196 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958196 Building ZINC001638958197 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638958197 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/882 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/882' -> `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(CCCC2)OC[C@H]1C) `ZINC001638958197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638958197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638958197 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 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, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 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, 57]) total number of confs: 67 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/883 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/883' -> `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(CCCC2)OC[C@H]1C) `ZINC001638958197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638958197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638958197 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 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, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 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, 57]) total number of confs: 67 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638958197 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 Building ZINC001638958197 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638958197 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 882) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[C@H]1C) `ZINC001638958197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638958197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638958197 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 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, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 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, 57]) total number of confs: 67 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 883) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[C@H]1C) `ZINC001638958197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638958197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001638958197 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC2(CCCC2)OC[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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 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, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 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, 57]) total number of confs: 67 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638958197 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638958197 Building ZINC001638959808 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638959808 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/884 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ncc(Br)cn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638959808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638959808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638959808 none O=C(N1CCC[C@@H]1c1ncc(Br)cn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 17, 1, 8, 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, 3, 7, 7, 7, 7, 3, 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: [9, 1, 9, 17, 17, 17, 17, 17, 17, 44, 44, 19, 44, 44, 44, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 44, 44, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/885 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ncc(Br)cn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638959808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638959808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638959808 none O=C(N1CCC[C@@H]1c1ncc(Br)cn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 17, 1, 8, 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, 3, 7, 7, 7, 7, 3, 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: [9, 1, 9, 16, 16, 16, 16, 16, 16, 46, 46, 24, 46, 46, 46, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 46, 46, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638959808 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 Building ZINC001638959808 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638959808 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 884) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ncc(Br)cn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638959808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638959808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638959808 none O=C(N1CCC[C@@H]1c1ncc(Br)cn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 17, 1, 8, 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, 3, 7, 7, 7, 7, 3, 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: [9, 1, 9, 17, 17, 17, 17, 17, 17, 44, 44, 19, 44, 44, 44, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 44, 44, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 885) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1ncc(Br)cn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638959808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638959808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638959808 none O=C(N1CCC[C@@H]1c1ncc(Br)cn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 17, 1, 8, 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, 3, 7, 7, 7, 7, 3, 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: [9, 1, 9, 16, 16, 16, 16, 16, 16, 46, 46, 24, 46, 46, 46, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 46, 46, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638959808 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959808 Building ZINC001638959809 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638959809 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/886 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1ncc(Br)cn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638959809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638959809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638959809 none O=C(N1CCC[C@H]1c1ncc(Br)cn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 17, 1, 8, 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, 3, 7, 7, 7, 7, 3, 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: [9, 1, 9, 15, 15, 15, 15, 15, 15, 46, 46, 20, 44, 46, 46, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 46, 46, 5, 1, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/887 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1ncc(Br)cn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638959809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638959809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638959809 none O=C(N1CCC[C@H]1c1ncc(Br)cn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 17, 1, 8, 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, 3, 7, 7, 7, 7, 3, 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: [9, 1, 9, 17, 17, 17, 17, 17, 17, 46, 46, 46, 46, 46, 46, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 46, 46, 5, 2, 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]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638959809 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 Building ZINC001638959809 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638959809 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 886) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@H]1c1ncc(Br)cn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638959809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638959809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638959809 none O=C(N1CCC[C@H]1c1ncc(Br)cn1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 17, 1, 8, 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, 3, 7, 7, 7, 7, 3, 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: [9, 1, 9, 15, 15, 15, 15, 15, 15, 46, 46, 20, 44, 46, 46, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 46, 46, 5, 1, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 887) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@H]1c1ncc(Br)cn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001638959809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638959809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001638959809 none O=C(N1CCC[C@H]1c1ncc(Br)cn1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 17, 1, 8, 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, 3, 7, 7, 7, 7, 3, 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: [9, 1, 9, 17, 17, 17, 17, 17, 17, 46, 46, 46, 46, 46, 46, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 46, 46, 5, 2, 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]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638959809 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638959809 Building ZINC001638999221 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638999221 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/888 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H]1c1ccccc1) `ZINC001638999221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638999221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001638999221 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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, 3, 7, 5, 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, 7] 0 hydrogens 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, 7, 27, 7, 7, 7, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 12, 12, 7, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 3, 3, 3, 3, 7, 7, 12, 12, 7, 12, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/889 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H]1c1ccccc1) `ZINC001638999221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638999221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001638999221 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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, 3, 7, 5, 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, 7] 0 hydrogens 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, 6, 34, 6, 6, 6, 1, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 10, 10, 6, 10, 10, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 3, 3, 3, 3, 6, 6, 10, 10, 6, 10, 10] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 102 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638999221 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 Building ZINC001638999221 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001638999221 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 888) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H]1c1ccccc1) `ZINC001638999221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001638999221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001638999221 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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, 3, 7, 5, 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, 7] 0 hydrogens 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, 7, 27, 7, 7, 7, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 12, 12, 7, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 3, 3, 3, 3, 7, 7, 12, 12, 7, 12, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 889) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H]1c1ccccc1) `ZINC001638999221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001638999221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001638999221 none CC(C)(C)OC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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, 3, 7, 5, 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, 7] 0 hydrogens 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, 6, 34, 6, 6, 6, 1, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 10, 10, 6, 10, 10, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 3, 3, 3, 3, 6, 6, 10, 10, 6, 10, 10] 50 rigid atoms, others: [10, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 102 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001638999221 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001638999221 Building ZINC001639098705 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639098705 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/890 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001639098705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639098705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639098705 none C[C@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 18, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [21, 21, 21, 45, 45, 45, 45, 45, 45, 45, 21, 21, 21, 8, 2, 12, 1, 1, 1, 6, 6, 3, 6, 6, 21, 21, 21, 45, 45, 45, 45, 45, 45, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6] 46 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]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/891 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001639098705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639098705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639098705 none C[C@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 18, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 41, 41, 41, 41, 41, 41, 41, 20, 20, 20, 8, 2, 13, 1, 1, 1, 6, 6, 1, 6, 6, 20, 20, 20, 41, 41, 41, 41, 41, 41, 20, 20, 20, 20, 20, 20, 6, 6, 1, 6, 6] 42 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639098705 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 Building ZINC001639098705 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639098705 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 890) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001639098705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639098705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639098705 none C[C@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 18, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [21, 21, 21, 45, 45, 45, 45, 45, 45, 45, 21, 21, 21, 8, 2, 12, 1, 1, 1, 6, 6, 3, 6, 6, 21, 21, 21, 45, 45, 45, 45, 45, 45, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6] 46 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]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 891) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001639098705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639098705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639098705 none C[C@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 18, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 41, 41, 41, 41, 41, 41, 41, 20, 20, 20, 8, 2, 13, 1, 1, 1, 6, 6, 1, 6, 6, 20, 20, 20, 41, 41, 41, 41, 41, 41, 20, 20, 20, 20, 20, 20, 6, 6, 1, 6, 6] 42 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639098705 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098705 Building ZINC001639098704 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639098704 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/892 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001639098704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639098704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639098704 none C[C@@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 18, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 40, 40, 40, 40, 40, 40, 40, 20, 20, 20, 8, 2, 13, 1, 1, 1, 6, 6, 1, 6, 6, 20, 20, 20, 40, 40, 40, 40, 40, 40, 20, 20, 20, 20, 20, 20, 6, 6, 1, 6, 6] 41 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/893 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001639098704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639098704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639098704 none C[C@@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 18, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [21, 21, 21, 45, 45, 45, 45, 45, 45, 45, 21, 21, 21, 8, 2, 12, 1, 1, 1, 6, 6, 1, 6, 6, 21, 21, 21, 45, 45, 45, 45, 45, 45, 21, 21, 21, 21, 21, 21, 6, 6, 1, 6, 6] 46 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]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639098704 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 Building ZINC001639098704 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639098704 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 892) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001639098704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639098704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639098704 none C[C@@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 18, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 40, 40, 40, 40, 40, 40, 40, 20, 20, 20, 8, 2, 13, 1, 1, 1, 6, 6, 1, 6, 6, 20, 20, 20, 40, 40, 40, 40, 40, 40, 20, 20, 20, 20, 20, 20, 6, 6, 1, 6, 6] 41 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 893) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001639098704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639098704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001639098704 none C[C@@]1(Cc2ccc(I)cc2)CCCN1C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 18, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [21, 21, 21, 45, 45, 45, 45, 45, 45, 45, 21, 21, 21, 8, 2, 12, 1, 1, 1, 6, 6, 1, 6, 6, 21, 21, 21, 45, 45, 45, 45, 45, 45, 21, 21, 21, 21, 21, 21, 6, 6, 1, 6, 6] 46 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]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639098704 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639098704 Building ZINC001639319048 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639319048 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/894 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](CCNC(=O)OC(C)(C)C)c2ccccc21) `ZINC001639319048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639319048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001639319048 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](CCNC(=O)OC(C)(C)C)c2ccccc21 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', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 6, 10, 32, 49, 49, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 10, 10, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/895 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](CCNC(=O)OC(C)(C)C)c2ccccc21) `ZINC001639319048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639319048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001639319048 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](CCNC(=O)OC(C)(C)C)c2ccccc21 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', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 8, 11, 38, 48, 48, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 11, 11, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 2, 35, 4, 5, 37, 36] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639319048 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 Building ZINC001639319048 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639319048 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 894) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](CCNC(=O)OC(C)(C)C)c2ccccc21) `ZINC001639319048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639319048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001639319048 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](CCNC(=O)OC(C)(C)C)c2ccccc21 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', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 6, 10, 32, 49, 49, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 10, 10, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 10, 2, 35, 4, 5, 37, 36] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 895) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](CCNC(=O)OC(C)(C)C)c2ccccc21) `ZINC001639319048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639319048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001639319048 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](CCNC(=O)OC(C)(C)C)c2ccccc21 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', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 8, 11, 38, 48, 48, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 11, 11, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 2, 35, 4, 5, 37, 36] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639319048 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319048 Building ZINC001639319049 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639319049 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/896 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CCNC(=O)OC(C)(C)C)c2ccccc21) `ZINC001639319049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639319049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001639319049 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CCNC(=O)OC(C)(C)C)c2ccccc21 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', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 8, 12, 37, 48, 48, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 12, 12, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 2, 35, 4, 5, 37, 36] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/897 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CCNC(=O)OC(C)(C)C)c2ccccc21) `ZINC001639319049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639319049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001639319049 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CCNC(=O)OC(C)(C)C)c2ccccc21 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', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 7, 11, 32, 47, 47, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 11, 11, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 2, 35, 4, 5, 37, 36] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639319049 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 Building ZINC001639319049 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639319049 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 896) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CCNC(=O)OC(C)(C)C)c2ccccc21) `ZINC001639319049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639319049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001639319049 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CCNC(=O)OC(C)(C)C)c2ccccc21 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', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 8, 12, 37, 48, 48, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 12, 12, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 2, 35, 4, 5, 37, 36] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 897) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CCNC(=O)OC(C)(C)C)c2ccccc21) `ZINC001639319049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639319049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001639319049 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CCNC(=O)OC(C)(C)C)c2ccccc21 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', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 7, 11, 32, 47, 47, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 11, 11, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 33, 6, 7, 8, 9, 2, 35, 4, 5, 37, 36] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639319049 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639319049 Building ZINC001639441414 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639441414 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/898 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639441414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639441414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001639441414 none O=C(N1CCC[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', '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'] dock atom type numbers: [11, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 11, 18, 31, 31, 25, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 18, 18, 31, 31, 28, 31, 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]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/899 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639441414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639441414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001639441414 none O=C(N1CCC[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', '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'] dock atom type numbers: [11, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 10, 10, 10, 10, 10, 17, 31, 31, 22, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 17, 17, 31, 31, 26, 31, 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]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639441414 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 Building ZINC001639441414 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639441414 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 898) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639441414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639441414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001639441414 none O=C(N1CCC[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', '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'] dock atom type numbers: [11, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 11, 18, 31, 31, 25, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 18, 18, 31, 31, 28, 31, 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]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 899) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639441414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639441414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001639441414 none O=C(N1CCC[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', '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'] dock atom type numbers: [11, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 10, 10, 10, 10, 10, 17, 31, 31, 22, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 17, 17, 31, 31, 26, 31, 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]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639441414 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441414 Building ZINC001639441415 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639441415 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/900 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639441415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639441415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001639441415 none O=C(N1CCC[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', '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'] dock atom type numbers: [11, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 10, 10, 10, 10, 10, 16, 30, 30, 20, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 16, 16, 30, 30, 25, 30, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/901 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639441415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639441415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001639441415 none O=C(N1CCC[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', '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'] dock atom type numbers: [11, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 11, 17, 32, 32, 23, 32, 32, 32, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 17, 17, 32, 32, 29, 32, 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]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639441415 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 Building ZINC001639441415 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639441415 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 900) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639441415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639441415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001639441415 none O=C(N1CCC[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', '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'] dock atom type numbers: [11, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 10, 10, 10, 10, 10, 16, 30, 30, 20, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 16, 16, 30, 30, 25, 30, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 901) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639441415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639441415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001639441415 none O=C(N1CCC[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', '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'] dock atom type numbers: [11, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 11, 11, 11, 17, 32, 32, 23, 32, 32, 32, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 17, 17, 32, 32, 29, 32, 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]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639441415 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639441415 Building ZINC001639658802 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639658802 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/902 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)OCc1ccccc1) `ZINC001639658802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639658802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639658802 none O=C(NCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)OCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 33, 33, 50, 50, 50, 50, 50, 50, 23, 6, 6, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/903 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)OCc1ccccc1) `ZINC001639658802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639658802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639658802 none O=C(NCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)OCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 32, 32, 50, 50, 50, 50, 50, 50, 21, 14, 14, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639658802 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 Building ZINC001639658802 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639658802 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 902) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)OCc1ccccc1) `ZINC001639658802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639658802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639658802 none O=C(NCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)OCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 33, 33, 50, 50, 50, 50, 50, 50, 23, 6, 6, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 903) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)OCc1ccccc1) `ZINC001639658802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639658802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001639658802 none O=C(NCC1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1)OCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 32, 32, 50, 50, 50, 50, 50, 50, 21, 14, 14, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [38, 39, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639658802 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639658802 Building ZINC001639679147 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639679147 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/904 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC2(CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2) `ZINC001639679147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639679147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001639679147 none C[C@H]1CC2(CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 11, 11, 12, 11, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 18, 18, 24, 25, 25, 25, 12, 12, 11, 11, 11, 11, 12, 10, 12, 5, 5, 5, 5, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/905 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC2(CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2) `ZINC001639679147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639679147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001639679147 none C[C@H]1CC2(CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 20, 20, 31, 33, 33, 33, 12, 12, 12, 12, 12, 12, 12, 12, 10, 3, 3, 3, 3, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639679147 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 Building ZINC001639679147 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639679147 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 904) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC2(CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2) `ZINC001639679147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639679147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001639679147 none C[C@H]1CC2(CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 11, 11, 12, 11, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 18, 18, 24, 25, 25, 25, 12, 12, 11, 11, 11, 11, 12, 10, 12, 5, 5, 5, 5, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 905) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC2(CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2) `ZINC001639679147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639679147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001639679147 none C[C@H]1CC2(CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 20, 20, 31, 33, 33, 33, 12, 12, 12, 12, 12, 12, 12, 12, 10, 3, 3, 3, 3, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639679147 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679147 Building ZINC001639679148 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639679148 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/906 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC2(CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2) `ZINC001639679148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639679148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001639679148 none C[C@@H]1CC2(CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 18, 18, 31, 32, 32, 32, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/907 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CC2(CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2) `ZINC001639679148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639679148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001639679148 none C[C@@H]1CC2(CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 19, 19, 24, 25, 25, 25, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639679148 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 Building ZINC001639679148 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639679148 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 906) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CC2(CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2) `ZINC001639679148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639679148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001639679148 none C[C@@H]1CC2(CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 18, 18, 31, 32, 32, 32, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 907) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@@H]1CC2(CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2) `ZINC001639679148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639679148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001639679148 none C[C@@H]1CC2(CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c3cc(F)ccc31)CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 19, 19, 24, 25, 25, 25, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639679148 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639679148 Building ZINC001639690499 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639690499 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/908 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001639690499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639690499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001639690499 none CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 15, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2] 150 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/909 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001639690499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639690499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001639690499 none CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 15, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2] 150 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]) total number of confs: 127 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639690499 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 Building ZINC001639690499 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639690499 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 908) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001639690499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639690499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001639690499 none CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 15, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2] 150 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 909) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001639690499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639690499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001639690499 none CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 15, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2] 150 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]) total number of confs: 127 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639690499 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639690499 Building ZINC001639717966 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639717966 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/910 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639717966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639717966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001639717966 none O=C(N1CCc2c(Cl)ccc(Br)c2C1)[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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 16, 1, 1, 1, 17, 1, 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, 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: [7, 2, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 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, 35, 36, 37, 38]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/911 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639717966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639717966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001639717966 none O=C(N1CCc2c(Cl)ccc(Br)c2C1)[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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 16, 1, 1, 1, 17, 1, 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, 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: [7, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 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, 35, 36, 37, 38]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639717966 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 Building ZINC001639717966 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639717966 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 910) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639717966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639717966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001639717966 none O=C(N1CCc2c(Cl)ccc(Br)c2C1)[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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 16, 1, 1, 1, 17, 1, 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, 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: [7, 2, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 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, 35, 36, 37, 38]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 911) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: O=C(N1CCc2c(Cl)ccc(Br)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001639717966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639717966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001639717966 none O=C(N1CCc2c(Cl)ccc(Br)c2C1)[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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 16, 1, 1, 1, 17, 1, 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, 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: [7, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 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, 35, 36, 37, 38]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639717966 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639717966 Building ZINC001639768188 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639768188 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/912 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1) `ZINC001639768188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639768188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001639768188 none CC[C@@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 17, 19, 19, 19, 4, 4, 4, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 2, 2, 4, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 2, 2, 2, 9, 9, 2, 9, 9, 2, 2, 2, 4, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 83 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/913 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1) `ZINC001639768188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639768188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001639768188 none CC[C@@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 27, 27, 27, 27, 6, 6, 6, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 6, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 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, 59, 60, 61, 62, 63, 64]) total number of confs: 88 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639768188 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 Building ZINC001639768188 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639768188 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 912) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC[C@@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1) `ZINC001639768188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639768188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001639768188 none CC[C@@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 17, 19, 19, 19, 4, 4, 4, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 2, 2, 4, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 2, 2, 2, 9, 9, 2, 9, 9, 2, 2, 2, 4, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 83 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 913) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC[C@@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1) `ZINC001639768188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639768188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001639768188 none CC[C@@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 27, 27, 27, 27, 6, 6, 6, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 6, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 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, 59, 60, 61, 62, 63, 64]) total number of confs: 88 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639768188 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768188 Building ZINC001639768190 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639768190 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/914 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1) `ZINC001639768190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639768190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001639768190 none CC[C@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 8, 8, 21, 21, 29, 29, 29, 29, 8, 8, 8, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 8, 13, 13, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 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, 59, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/915 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1) `ZINC001639768190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639768190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001639768190 none CC[C@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 6, 6, 14, 18, 18, 18, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 3, 10, 10, 2, 2, 3, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 2, 2, 2, 10, 10, 4, 10, 10, 2, 2, 2, 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, 40, 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: 91 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639768190 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 Building ZINC001639768190 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639768190 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 914) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC[C@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1) `ZINC001639768190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639768190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001639768190 none CC[C@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 8, 8, 21, 21, 29, 29, 29, 29, 8, 8, 8, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 8, 13, 13, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 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, 59, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 915) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC[C@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1) `ZINC001639768190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639768190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001639768190 none CC[C@]1(C(=O)OC(C)(C)C)CCCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 6, 6, 14, 18, 18, 18, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 3, 10, 10, 2, 2, 3, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 2, 2, 2, 10, 10, 4, 10, 10, 2, 2, 2, 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, 40, 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: 91 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639768190 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639768190 Building ZINC001639784046 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639784046 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/916 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1cc(F)c(OC)cc1F) `ZINC001639784046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639784046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001639784046 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1cc(F)c(OC)cc1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 15, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 24, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 24, 24, 24, 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, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/917 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1cc(F)c(OC)cc1F) `ZINC001639784046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639784046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001639784046 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1cc(F)c(OC)cc1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 15, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 24, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 24, 24, 24, 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, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639784046 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 Building ZINC001639784046 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639784046 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 916) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1cc(F)c(OC)cc1F) `ZINC001639784046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639784046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001639784046 none CCCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1cc(F)c(OC)cc1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 15, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 24, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 24, 24, 24, 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, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 917) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1cc(F)c(OC)cc1F) `ZINC001639784046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639784046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001639784046 none CCCc1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cnn1c1cc(F)c(OC)cc1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 15, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 24, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 24, 24, 24, 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, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639784046 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639784046 Building ZINC001639980631 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639980631 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/918 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001639980631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639980631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001639980631 none CC(C)(C)OC(=O)NCCCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)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.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 20, 5, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 5, 5, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/919 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCCCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001639980631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639980631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001639980631 none CC(C)(C)OC(=O)NCCCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)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.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 11, 18, 5, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 5, 5, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639980631 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 Building ZINC001639980631 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639980631 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 918) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NCCCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001639980631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639980631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001639980631 none CC(C)(C)OC(=O)NCCCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)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.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 20, 5, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 5, 5, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 919) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)NCCCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001639980631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639980631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001639980631 none CC(C)(C)OC(=O)NCCCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)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.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 11, 18, 5, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 5, 5, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 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, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639980631 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639980631 Building ZINC001639996460 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639996460 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/920 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Oc2cccc(Cl)c2Cl)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001639996460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639996460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001639996460 none O=C(N1CC(Oc2cccc(Cl)c2Cl)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 6, 6, 6, 24, 39, 39, 35, 39, 39, 39, 39, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 39, 39, 39, 6, 6, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/921 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Oc2cccc(Cl)c2Cl)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001639996460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639996460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001639996460 none O=C(N1CC(Oc2cccc(Cl)c2Cl)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 5, 5, 5, 22, 37, 37, 35, 37, 37, 37, 37, 5, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 37, 37, 37, 5, 5, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639996460 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 Building ZINC001639996460 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639996460 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 920) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Oc2cccc(Cl)c2Cl)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001639996460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639996460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001639996460 none O=C(N1CC(Oc2cccc(Cl)c2Cl)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 6, 6, 6, 24, 39, 39, 35, 39, 39, 39, 39, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 39, 39, 39, 6, 6, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 921) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Oc2cccc(Cl)c2Cl)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001639996460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639996460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001639996460 none O=C(N1CC(Oc2cccc(Cl)c2Cl)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 5, 5, 5, 22, 37, 37, 35, 37, 37, 37, 37, 5, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 37, 37, 37, 5, 5, 3, 3] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639996460 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639996460 Building ZINC001639999431 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639999431 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/922 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n[nH]1) `ZINC001639999431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639999431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001639999431 none COc1ccc(Cl)cc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [33, 31, 31, 31, 13, 31, 31, 31, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 33, 33, 33, 31, 31, 31, 8, 4, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/923 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cl)cc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n[nH]1) `ZINC001639999431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639999431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001639999431 none COc1ccc(Cl)cc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [33, 32, 32, 32, 8, 32, 32, 32, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 33, 33, 33, 32, 32, 32, 8, 4, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639999431 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 Building ZINC001639999431 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001639999431 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 922) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(Cl)cc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n[nH]1) `ZINC001639999431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001639999431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001639999431 none COc1ccc(Cl)cc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [33, 31, 31, 31, 13, 31, 31, 31, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 33, 33, 33, 31, 31, 31, 8, 4, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 923) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc(Cl)cc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n[nH]1) `ZINC001639999431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001639999431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001639999431 none COc1ccc(Cl)cc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [33, 32, 32, 32, 8, 32, 32, 32, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 33, 33, 33, 32, 32, 32, 8, 4, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001639999431 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001639999431 Building ZINC001640342358 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640342358 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/924 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001640342358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640342358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001640342358 none CC(C)(C)OC(=O)N1CC[C@@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 15, 28, 15, 15, 15, 15, 15, 15, 15, 7, 1, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 2, 15, 15] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/925 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001640342358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640342358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001640342358 none CC(C)(C)OC(=O)N1CC[C@@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 15, 29, 15, 15, 15, 15, 15, 15, 15, 8, 2, 9, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 2, 15, 15] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640342358 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 Building ZINC001640342358 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640342358 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 924) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001640342358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640342358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001640342358 none CC(C)(C)OC(=O)N1CC[C@@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 15, 28, 15, 15, 15, 15, 15, 15, 15, 7, 1, 8, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 2, 15, 15] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 925) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001640342358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640342358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001640342358 none CC(C)(C)OC(=O)N1CC[C@@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 15, 29, 15, 15, 15, 15, 15, 15, 15, 8, 2, 9, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 2, 15, 15] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640342358 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342358 Building ZINC001640342359 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640342359 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/926 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001640342359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640342359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001640342359 none CC(C)(C)OC(=O)N1CC[C@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 13, 28, 13, 13, 13, 13, 13, 13, 13, 8, 4, 6, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 1, 2, 13, 13] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/927 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001640342359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640342359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001640342359 none CC(C)(C)OC(=O)N1CC[C@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 12, 26, 12, 12, 12, 12, 12, 12, 12, 7, 3, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 3, 12, 12] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640342359 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 Building ZINC001640342359 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640342359 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 926) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001640342359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640342359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001640342359 none CC(C)(C)OC(=O)N1CC[C@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 13, 28, 13, 13, 13, 13, 13, 13, 13, 8, 4, 6, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 1, 2, 13, 13] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 927) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CC[C@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001640342359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640342359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001640342359 none CC(C)(C)OC(=O)N1CC[C@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 12, 26, 12, 12, 12, 12, 12, 12, 12, 7, 3, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 3, 12, 12] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640342359 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640342359 Building ZINC001640470256 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640470256 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/928 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc3cccnc3n2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001640470256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640470256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001640470256 none O=C(N1CCC(c2ccc3cccnc3n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 11, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 15, 15, 15, 15, 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: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/929 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc3cccnc3n2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001640470256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640470256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001640470256 none O=C(N1CCC(c2ccc3cccnc3n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 9, 12, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 12, 12, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 36, 36, 36, 36, 36, 12, 12, 12, 12, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640470256 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 Building ZINC001640470256 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640470256 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 928) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CCC(c2ccc3cccnc3n2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001640470256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640470256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001640470256 none O=C(N1CCC(c2ccc3cccnc3n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 11, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 15, 15, 15, 15, 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: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 929) grep: /scratch/xiaobo/369383/xbb-8058088.28/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(N1CCC(c2ccc3cccnc3n2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001640470256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640470256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001640470256 none O=C(N1CCC(c2ccc3cccnc3n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 9, 12, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 12, 12, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 36, 36, 36, 36, 36, 12, 12, 12, 12, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640470256 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640470256 Building ZINC001640513004 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640513004 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/930 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCn1ccnc1)Cc1ccccc1Br) `ZINC001640513004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640513004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001640513004 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCn1ccnc1)Cc1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 11, 26, 26, 26, 26, 5, 13, 21, 21, 13, 21, 21, 21, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 26, 13, 13, 21, 21, 17, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/931 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCn1ccnc1)Cc1ccccc1Br) `ZINC001640513004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640513004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001640513004 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCn1ccnc1)Cc1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 11, 26, 26, 26, 26, 5, 13, 21, 21, 18, 21, 21, 21, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 26, 13, 13, 21, 21, 18, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640513004 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 Building ZINC001640513004 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640513004 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 930) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCn1ccnc1)Cc1ccccc1Br) `ZINC001640513004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640513004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001640513004 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(CCn1ccnc1)Cc1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 11, 26, 26, 26, 26, 5, 13, 21, 21, 13, 21, 21, 21, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 26, 13, 13, 21, 21, 17, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 931) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCn1ccnc1)Cc1ccccc1Br) `ZINC001640513004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640513004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001640513004 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(CCn1ccnc1)Cc1ccccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 11, 26, 26, 26, 26, 5, 13, 21, 21, 18, 21, 21, 21, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 26, 13, 13, 21, 21, 18, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640513004 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640513004 Building ZINC001640695685 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640695685 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/932 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001640695685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640695685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001640695685 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 28, 28, 32, 32, 32, 32, 24, 4, 4, 4, 9, 9, 9, 4, 4, 2, 24, 24, 24, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 24, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/933 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001640695685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640695685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001640695685 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 28, 28, 28, 28, 19, 4, 4, 4, 8, 8, 8, 4, 4, 3, 19, 19, 19, 19, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 19, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640695685 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 Building ZINC001640695685 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640695685 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 932) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001640695685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640695685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001640695685 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 28, 28, 32, 32, 32, 32, 24, 4, 4, 4, 9, 9, 9, 4, 4, 2, 24, 24, 24, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 24, 24, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 933) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001640695685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640695685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001640695685 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 28, 28, 28, 28, 19, 4, 4, 4, 8, 8, 8, 4, 4, 3, 19, 19, 19, 19, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 19, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640695685 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695685 Building ZINC001640695686 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640695686 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/934 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001640695686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640695686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001640695686 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 20, 20, 26, 26, 26, 26, 18, 5, 5, 5, 9, 9, 9, 5, 5, 3, 18, 18, 18, 18, 18, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/935 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001640695686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640695686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001640695686 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 2, 2, 4, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 24, 24, 28, 28, 28, 28, 20, 5, 5, 5, 10, 10, 10, 5, 5, 2, 20, 20, 20, 20, 20, 20, 28, 28, 28, 28, 28, 28, 28, 28, 28, 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640695686 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 Building ZINC001640695686 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640695686 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 934) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)N[C@@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001640695686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640695686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001640695686 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 20, 20, 26, 26, 26, 26, 18, 5, 5, 5, 9, 9, 9, 5, 5, 3, 18, 18, 18, 18, 18, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 18, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 935) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)N[C@@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001640695686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640695686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001640695686 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3N(C(=O)OC(C)(C)C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 5, 1, 1, 1, 1, 2, 2, 4, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 24, 24, 28, 28, 28, 28, 20, 5, 5, 5, 10, 10, 10, 5, 5, 2, 20, 20, 20, 20, 20, 20, 28, 28, 28, 28, 28, 28, 28, 28, 28, 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640695686 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640695686 Building ZINC001640870971 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640870971 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/936 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2) `ZINC001640870971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640870971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870971 none CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 26, 6, 5, 5, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 6, 6, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/937 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2) `ZINC001640870971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640870971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870971 none CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 15, 23, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 7, 7, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640870971 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 Building ZINC001640870971 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640870971 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 936) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2) `ZINC001640870971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640870971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870971 none CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 26, 6, 5, 5, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 6, 6, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 937) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2) `ZINC001640870971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640870971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870971 none CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 15, 23, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 7, 7, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640870971 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870971 Building ZINC001640870972 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640870972 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/938 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2) `ZINC001640870972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640870972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870972 none CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 21, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 14, 7, 7, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/939 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2) `ZINC001640870972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640870972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870972 none CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 27, 18, 27, 7, 5, 5, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 7, 7, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640870972 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 Building ZINC001640870972 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640870972 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 938) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2) `ZINC001640870972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640870972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870972 none CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 21, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 14, 7, 7, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 939) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2) `ZINC001640870972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640870972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870972 none CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 27, 18, 27, 7, 5, 5, 5, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 7, 7, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640870972 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870972 Building ZINC001640870973 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640870973 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/940 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2) `ZINC001640870973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640870973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870973 none CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 26, 9, 3, 3, 3, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/941 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2) `ZINC001640870973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640870973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870973 none CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 33, 22, 33, 9, 4, 4, 4, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 22, 9, 9, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640870973 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 Building ZINC001640870973 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640870973 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 940) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2) `ZINC001640870973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640870973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870973 none CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 26, 9, 3, 3, 3, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 941) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2) `ZINC001640870973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640870973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870973 none CC(C)(C)OC(=O)NC[C@@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 33, 22, 33, 9, 4, 4, 4, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 22, 9, 9, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640870973 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870973 Building ZINC001640870974 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640870974 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/942 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2) `ZINC001640870974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640870974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870974 none CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 34, 23, 34, 10, 4, 4, 4, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 23, 10, 10, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/943 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2) `ZINC001640870974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640870974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870974 none CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 28, 18, 28, 10, 3, 3, 3, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640870974 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 Building ZINC001640870974 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001640870974 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 942) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)NC[C@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2) `ZINC001640870974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001640870974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870974 none CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 34, 23, 34, 10, 4, 4, 4, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 23, 10, 10, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 943) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)NC[C@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2) `ZINC001640870974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001640870974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001640870974 none CC(C)(C)OC(=O)NC[C@]12CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]1CCCC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 28, 18, 28, 10, 3, 3, 3, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 11, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001640870974 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001640870974 Building ZINC001641052840 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641052840 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/944 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](c2ccc(Br)cc2)OCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001641052840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641052840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001641052840 none C[C@H]1[C@H](c2ccc(Br)cc2)OCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 7, 1, 1, 1, 1, 17, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 26, 26, 23, 26, 26, 26, 19, 19, 19, 13, 2, 13, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 26, 26, 26, 26, 19, 19, 19, 19, 8, 8, 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, 42, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/945 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](c2ccc(Br)cc2)OCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001641052840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641052840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001641052840 none C[C@H]1[C@H](c2ccc(Br)cc2)OCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 7, 1, 1, 1, 1, 17, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 26, 26, 25, 26, 26, 26, 19, 19, 19, 14, 2, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 26, 26, 26, 26, 19, 19, 19, 19, 7, 7, 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, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641052840 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 Building ZINC001641052840 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641052840 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 944) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1[C@H](c2ccc(Br)cc2)OCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001641052840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641052840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001641052840 none C[C@H]1[C@H](c2ccc(Br)cc2)OCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 7, 1, 1, 1, 1, 17, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 26, 26, 23, 26, 26, 26, 19, 19, 19, 13, 2, 13, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 26, 26, 26, 26, 19, 19, 19, 19, 8, 8, 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, 42, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 945) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: C[C@H]1[C@H](c2ccc(Br)cc2)OCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001641052840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641052840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001641052840 none C[C@H]1[C@H](c2ccc(Br)cc2)OCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 7, 1, 1, 1, 1, 17, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 26, 26, 25, 26, 26, 26, 19, 19, 19, 14, 2, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 26, 26, 26, 26, 19, 19, 19, 19, 7, 7, 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, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641052840 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641052840 Building ZINC001641105331 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641105331 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/946 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/946' -> `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(CCC(=O)OC(C)(C)C)CC1) `ZINC001641105331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641105331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001641105331 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CCC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 9, 40, 40, 42, 42, 42, 42, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 2, 2, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/947 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/947' -> `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(CCC(=O)OC(C)(C)C)CC1) `ZINC001641105331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641105331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001641105331 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CCC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 8, 10, 47, 47, 48, 48, 48, 48, 3, 3, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 3, 3, 3, 3, 3, 8, 8, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641105331 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 Building ZINC001641105331 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641105331 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 946) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CCC(=O)OC(C)(C)C)CC1) `ZINC001641105331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641105331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001641105331 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CCC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 9, 40, 40, 42, 42, 42, 42, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 9, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 2, 2, 2, 2] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 947) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CCC(=O)OC(C)(C)C)CC1) `ZINC001641105331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641105331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001641105331 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CCC(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 8, 10, 47, 47, 48, 48, 48, 48, 3, 3, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 3, 3, 3, 3, 3, 8, 8, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641105331 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641105331 Building ZINC001641164384 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641164384 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/948 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2)cc1) `ZINC001641164384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641164384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001641164384 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 45, 45, 23, 23, 23, 16, 12, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 45, 45, 45, 23, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50] 50 rigid atoms, others: [48, 51, 49, 50, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 54, 55, 56, 57]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/949 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2)cc1) `ZINC001641164384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641164384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001641164384 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 46, 46, 22, 22, 22, 15, 10, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 46, 22, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [48, 51, 49, 50, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 54, 55, 56, 57]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641164384 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 Building ZINC001641164384 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641164384 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 948) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2)cc1) `ZINC001641164384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641164384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001641164384 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 45, 45, 23, 23, 23, 16, 12, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 45, 45, 45, 45, 45, 45, 23, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50] 50 rigid atoms, others: [48, 51, 49, 50, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 54, 55, 56, 57]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 949) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2)cc1) `ZINC001641164384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641164384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001641164384 none Cc1ccc(OCCCC(=O)Nc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 46, 46, 22, 22, 22, 15, 10, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 46, 22, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [48, 51, 49, 50, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 54, 55, 56, 57]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641164384 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641164384 Building ZINC001641203215 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641203215 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/950 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c1c1ccc(Cl)cc1) `ZINC001641203215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641203215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641203215 none COCc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 3, 3, 6, 6, 5, 6, 6, 6, 16, 16, 16, 9, 9, 3, 6, 6, 12, 12, 12, 6, 6, 6, 6, 6] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/951 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c1c1ccc(Cl)cc1) `ZINC001641203215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641203215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641203215 none COCc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 5, 6, 12, 6, 6, 6, 3, 3, 6, 6, 5, 5, 6, 6, 17, 17, 17, 10, 10, 3, 6, 6, 12, 12, 12, 6, 6, 6, 6, 6] 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641203215 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 Building ZINC001641203215 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641203215 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 950) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COCc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c1c1ccc(Cl)cc1) `ZINC001641203215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641203215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641203215 none COCc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 3, 3, 6, 6, 5, 6, 6, 6, 16, 16, 16, 9, 9, 3, 6, 6, 12, 12, 12, 6, 6, 6, 6, 6] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 951) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COCc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c1c1ccc(Cl)cc1) `ZINC001641203215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641203215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641203215 none COCc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 5, 6, 12, 6, 6, 6, 3, 3, 6, 6, 5, 5, 6, 6, 17, 17, 17, 10, 10, 3, 6, 6, 12, 12, 12, 6, 6, 6, 6, 6] 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641203215 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641203215 Building ZINC001641219850 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641219850 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/952 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OCc2ccc(F)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001641219850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641219850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641219850 none O=C(N1CCC(OCc2ccc(F)cc2)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 5, 1, 1, 1, 1, 15, 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, 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, 37, 37, 31, 37, 37, 37, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 27, 27, 37, 37, 37, 37, 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/953 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OCc2ccc(F)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001641219850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641219850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641219850 none O=C(N1CCC(OCc2ccc(F)cc2)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 5, 1, 1, 1, 1, 15, 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, 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, 5, 5, 5, 5, 12, 35, 36, 36, 35, 36, 36, 36, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 35, 35, 36, 36, 36, 36, 5, 5, 5, 5, 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641219850 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 Building ZINC001641219850 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641219850 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 952) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OCc2ccc(F)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001641219850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641219850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641219850 none O=C(N1CCC(OCc2ccc(F)cc2)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 5, 1, 1, 1, 1, 15, 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, 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, 37, 37, 31, 37, 37, 37, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 27, 27, 37, 37, 37, 37, 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: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 953) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(OCc2ccc(F)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001641219850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641219850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641219850 none O=C(N1CCC(OCc2ccc(F)cc2)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 5, 1, 1, 1, 1, 15, 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, 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, 5, 5, 5, 5, 12, 35, 36, 36, 35, 36, 36, 36, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 35, 35, 36, 36, 36, 36, 5, 5, 5, 5, 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641219850 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641219850 Building ZINC001641222379 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641222379 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/954 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(Cc3nc(C4CCCCC4)no3)CC2)cc1Cl) `ZINC001641222379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641222379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001641222379 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(Cc3nc(C4CCCCC4)no3)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.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 6, 15, 15, 15, 30, 30, 30, 30, 30, 15, 15, 3, 3, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 3, 3, 3, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 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, 53, 54, 55, 56, 57, 58]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/955 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(Cc3nc(C4CCCCC4)no3)CC2)cc1Cl) `ZINC001641222379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641222379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001641222379 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(Cc3nc(C4CCCCC4)no3)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.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 29, 29, 29, 29, 29, 12, 12, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 3, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 38, 40, 57, 14, 54, 55, 56, 39, 26, 27, 37] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641222379 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 Building ZINC001641222379 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641222379 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 954) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(Cc3nc(C4CCCCC4)no3)CC2)cc1Cl) `ZINC001641222379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641222379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001641222379 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(Cc3nc(C4CCCCC4)no3)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.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 6, 15, 15, 15, 30, 30, 30, 30, 30, 15, 15, 3, 3, 2, 2, 2, 5, 5, 5, 2, 2, 3, 3, 3, 3, 3, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 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, 53, 54, 55, 56, 57, 58]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 955) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(Cc3nc(C4CCCCC4)no3)CC2)cc1Cl) `ZINC001641222379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641222379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001641222379 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(Cc3nc(C4CCCCC4)no3)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.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 29, 29, 29, 29, 29, 12, 12, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 3, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 2] 50 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 38, 40, 57, 14, 54, 55, 56, 39, 26, 27, 37] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641222379 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641222379 Building ZINC001641270654 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641270654 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/956 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nc3ccc(C(F)(F)F)cc3[nH]2)cc1Cl) `ZINC001641270654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641270654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001641270654 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nc3ccc(C(F)(F)F)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 7, 7, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 9, 9, 9, 6, 6, 7, 7, 7, 12, 12, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/957 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nc3ccc(C(F)(F)F)cc3[nH]2)cc1Cl) `ZINC001641270654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641270654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001641270654 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nc3ccc(C(F)(F)F)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 4, 6, 6, 1, 1, 1, 1, 2, 2, 7, 7, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 9, 9, 9, 6, 6, 7, 7, 7, 12, 12, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641270654 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 Building ZINC001641270654 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641270654 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 956) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nc3ccc(C(F)(F)F)cc3[nH]2)cc1Cl) `ZINC001641270654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641270654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001641270654 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)Cc2nc3ccc(C(F)(F)F)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 7, 7, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 9, 9, 9, 6, 6, 7, 7, 7, 12, 12, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 957) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nc3ccc(C(F)(F)F)cc3[nH]2)cc1Cl) `ZINC001641270654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641270654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001641270654 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)Cc2nc3ccc(C(F)(F)F)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 4, 6, 6, 1, 1, 1, 1, 2, 2, 7, 7, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 9, 9, 9, 6, 6, 7, 7, 7, 12, 12, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641270654 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641270654 Building ZINC001641274303 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641274303 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/958 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1csc(CC2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1) `ZINC001641274303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641274303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001641274303 none CC(C)(C)c1csc(CC2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 34, 34, 30, 30, 30, 11, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 34, 34, 34, 34, 34, 34, 34, 34, 34, 30, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/959 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1csc(CC2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1) `ZINC001641274303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641274303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001641274303 none CC(C)(C)c1csc(CC2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 11, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 11, 11, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641274303 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 Building ZINC001641274303 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641274303 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 958) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)c1csc(CC2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1) `ZINC001641274303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641274303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001641274303 none CC(C)(C)c1csc(CC2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 34, 34, 30, 30, 30, 11, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 34, 34, 34, 34, 34, 34, 34, 34, 34, 30, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 959) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)c1csc(CC2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1) `ZINC001641274303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641274303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001641274303 none CC(C)(C)c1csc(CC2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 11, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 11, 11, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641274303 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641274303 Building ZINC001641343125 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641343125 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/960 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1) `ZINC001641343125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641343125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001641343125 none CC(C)(C)OC(=O)N1CCC([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 19, 30, 19, 19, 19, 8, 8, 10, 8, 8, 8, 4, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 8, 19, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 8, 2, 2, 8, 8, 19, 19, 19, 19] 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, 57]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/961 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1) `ZINC001641343125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641343125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001641343125 none CC(C)(C)OC(=O)N1CCC([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 17, 27, 17, 17, 17, 6, 6, 7, 6, 6, 6, 5, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 3, 3, 6, 6, 17, 17, 17, 17] 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, 57]) total number of confs: 96 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641343125 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 Building ZINC001641343125 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641343125 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 960) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)OC(=O)N1CCC([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1) `ZINC001641343125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641343125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001641343125 none CC(C)(C)OC(=O)N1CCC([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 19, 30, 19, 19, 19, 8, 8, 10, 8, 8, 8, 4, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 8, 19, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 8, 2, 2, 8, 8, 19, 19, 19, 19] 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, 57]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 961) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)OC(=O)N1CCC([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1) `ZINC001641343125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641343125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001641343125 none CC(C)(C)OC(=O)N1CCC([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 17, 27, 17, 17, 17, 6, 6, 7, 6, 6, 6, 5, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 6, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 3, 3, 6, 6, 17, 17, 17, 17] 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, 57]) total number of confs: 96 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641343125 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343125 Building ZINC001641343126 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641343126 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/962 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1) `ZINC001641343126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641343126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001641343126 none CC(C)(C)OC(=O)N1CCC([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 18, 28, 18, 18, 18, 9, 9, 10, 9, 9, 9, 6, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 9, 18, 18, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 4, 4, 9, 9, 18, 18, 18, 18] 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, 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/369383/xbb-8058088.28/working/building/ZINC001641343126 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/963 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1) `ZINC001641343126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641343126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001641343126 none CC(C)(C)OC(=O)N1CCC([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 20, 30, 20, 20, 20, 9, 9, 11, 9, 9, 9, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 9, 20, 20, 38, 38, 38, 38, 38, 38, 38, 38, 38, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 9, 3, 3, 9, 9, 20, 20, 20, 20] 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, 57]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641343126 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126 Building ZINC001641343126 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641343126 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 962) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1) `ZINC001641343126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641343126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001641343126 none CC(C)(C)OC(=O)N1CCC([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 18, 28, 18, 18, 18, 9, 9, 10, 9, 9, 9, 6, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 9, 18, 18, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 4, 4, 9, 9, 18, 18, 18, 18] 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, 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/369383/xbb-8058088.28/working/building/ZINC001641343126 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 963) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1CCC([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1) `ZINC001641343126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641343126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001641343126 none CC(C)(C)OC(=O)N1CCC([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 20, 30, 20, 20, 20, 9, 9, 11, 9, 9, 9, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 9, 20, 20, 38, 38, 38, 38, 38, 38, 38, 38, 38, 20, 20, 20, 20, 20, 9, 9, 9, 9, 9, 9, 3, 3, 9, 9, 20, 20, 20, 20] 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, 57]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641343126 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641343126 Building ZINC001641401684 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641401684 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/964 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2C1) `ZINC001641401684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641401684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641401684 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom 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, 15, 1, 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, 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, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/965 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2C1) `ZINC001641401684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641401684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641401684 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom 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, 15, 1, 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, 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, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641401684 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 Building ZINC001641401684 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641401684 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 964) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2C1) `ZINC001641401684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641401684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641401684 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom 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, 15, 1, 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, 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, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 3, 18, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 965) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2C1) `ZINC001641401684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641401684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641401684 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccc(F)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom 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, 15, 1, 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, 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, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 2, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 18, 18, 5, 18, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641401684 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641401684 Building ZINC001641618331 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641618331 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/966 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001641618331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641618331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641618331 none CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 14, 28, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 14, 14] 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/967 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001641618331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641618331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641618331 none CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 19, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 19, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 19, 19] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641618331 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 Building ZINC001641618331 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641618331 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 966) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001641618331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641618331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641618331 none CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 14, 28, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 14, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 14, 14] 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 967) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001641618331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641618331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001641618331 none CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 19, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 19, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 4, 3, 3, 3, 3, 19, 19] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641618331 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618331 Building ZINC001641618561 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641618561 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/968 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001641618561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641618561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001641618561 none CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 13, 22, 13, 13, 13, 13, 13, 14, 14, 13, 14, 14, 6, 13, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 14, 14, 13, 14, 14, 3, 5, 5, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/969 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001641618561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641618561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001641618561 none CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 25, 14, 25, 14, 14, 14, 14, 14, 15, 15, 14, 15, 15, 6, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 15, 15, 14, 15, 15, 4, 6, 6, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641618561 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 Building ZINC001641618561 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641618561 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 968) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001641618561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641618561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001641618561 none CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 13, 22, 13, 13, 13, 13, 13, 14, 14, 13, 14, 14, 6, 13, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 14, 14, 13, 14, 14, 3, 5, 5, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 969) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC001641618561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641618561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001641618561 none CC(C)(C)OC(=O)N1C[C@@H](c2ccccc2)[C@H](NC(=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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 25, 14, 25, 14, 14, 14, 14, 14, 15, 15, 14, 15, 15, 6, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 15, 15, 14, 15, 15, 4, 6, 6, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641618561 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641618561 Building ZINC001641661247 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641661247 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/970 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ncco2)CC1) `ZINC001641661247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641661247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641661247 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ncco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 8, 1, 1, 12, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 7, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 10, 10, 10, 10, 4, 4, 2, 2, 2, 10, 10, 8, 10, 2, 2, 2, 4, 4, 4, 4, 4, 10, 10, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 40 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/971 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2ncco2)CC1) `ZINC001641661247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641661247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641661247 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2ncco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 8, 1, 1, 12, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 13, 13, 13, 13, 4, 4, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 4, 4, 4, 4, 4, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 46 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641661247 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 Building ZINC001641661247 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641661247 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 970) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ncco2)CC1) `ZINC001641661247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641661247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641661247 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ncco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 8, 1, 1, 12, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 7, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 10, 10, 10, 10, 4, 4, 2, 2, 2, 10, 10, 8, 10, 2, 2, 2, 4, 4, 4, 4, 4, 10, 10, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 40 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 971) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2ncco2)CC1) `ZINC001641661247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641661247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641661247 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2ncco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 8, 1, 1, 12, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 13, 13, 13, 13, 4, 4, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 4, 4, 4, 4, 4, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 46 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641661247 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641661247 Building ZINC001641705703 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641705703 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/972 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(C(=O)OC(C)(C)C)CCO2) `ZINC001641705703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641705703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001641705703 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(C(=O)OC(C)(C)C)CCO2 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.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 38, 38, 38, 20, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 2, 2, 2, 2, 2, 2, 4, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 54, 55]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/973 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(C(=O)OC(C)(C)C)CCO2) `ZINC001641705703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641705703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001641705703 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(C(=O)OC(C)(C)C)CCO2 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.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 21, 39, 39, 39, 21, 39, 39, 39, 50, 50, 50, 50, 50, 50, 39, 39, 39, 2, 2, 2, 2, 2, 2, 4, 39, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39] 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641705703 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 Building ZINC001641705703 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641705703 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 972) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(C(=O)OC(C)(C)C)CCO2) `ZINC001641705703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641705703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001641705703 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(C(=O)OC(C)(C)C)CCO2 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.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 38, 38, 38, 20, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 38, 38, 2, 2, 2, 2, 2, 2, 4, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 54, 55]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 973) grep: /scratch/xiaobo/369383/xbb-8058088.28/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(C(=O)OC(C)(C)C)CCO2) `ZINC001641705703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641705703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001641705703 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CN(C(=O)OC(C)(C)C)CCO2 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.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 21, 39, 39, 39, 21, 39, 39, 39, 50, 50, 50, 50, 50, 50, 39, 39, 39, 2, 2, 2, 2, 2, 2, 4, 39, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39] 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641705703 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641705703 Building ZINC001641759363 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641759363 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/974 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/974' -> `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(c2ccon2)CC1) `ZINC001641759363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641759363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641759363 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 1, 4, 6, 7, 7, 7, 7, 12, 12, 12, 12, 7, 7, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 7, 7, 7, 7, 7, 12, 12, 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: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/975 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/975' -> `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(c2ccon2)CC1) `ZINC001641759363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641759363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641759363 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 17, 17, 17, 17, 7, 7, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 7, 7, 7, 7, 7, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641759363 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 Building ZINC001641759363 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641759363 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 974) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1) `ZINC001641759363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641759363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641759363 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 1, 4, 6, 7, 7, 7, 7, 12, 12, 12, 12, 7, 7, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 7, 7, 7, 7, 7, 12, 12, 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: 52 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 975) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1) `ZINC001641759363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641759363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641759363 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccon2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 1, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 17, 17, 17, 17, 7, 7, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 7, 7, 7, 7, 7, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641759363 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641759363 Building ZINC001641819452 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641819452 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/976 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/976' -> `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)N1CCC2(CCCCO2)CC1) `ZINC001641819452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641819452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641819452 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/977 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/977' -> `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)N1CCC2(CCCCO2)CC1) `ZINC001641819452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641819452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641819452 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641819452 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 Building ZINC001641819452 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641819452 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 976) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCCO2)CC1) `ZINC001641819452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641819452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641819452 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC2(CCCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 977) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCCO2)CC1) `ZINC001641819452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641819452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001641819452 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC2(CCCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641819452 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641819452 Building ZINC001641927434 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641927434 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/978 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cccc(c2cn3c(n2)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC3)c1) `ZINC001641927434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641927434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001641927434 none CC(C)(C)OC(=O)Nc1cccc(c2cn3c(n2)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 49, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 21, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 21] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/369383/xbb-8058088.28/working/building/ZINC001641927434 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/979 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cccc(c2cn3c(n2)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC3)c1) `ZINC001641927434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641927434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001641927434 none CC(C)(C)OC(=O)Nc1cccc(c2cn3c(n2)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 45, 49, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 19] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641927434 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434 Building ZINC001641927434 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001641927434 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 978) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)Nc1cccc(c2cn3c(n2)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC3)c1) `ZINC001641927434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001641927434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001641927434 none CC(C)(C)OC(=O)Nc1cccc(c2cn3c(n2)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 49, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 21, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 21] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/369383/xbb-8058088.28/working/building/ZINC001641927434 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 979) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)Nc1cccc(c2cn3c(n2)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC3)c1) `ZINC001641927434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001641927434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001641927434 none CC(C)(C)OC(=O)Nc1cccc(c2cn3c(n2)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 45, 49, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 19] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001641927434 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001641927434 Building ZINC001642031505 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642031505 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/980 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2c(C)[nH]nc2NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001642031505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642031505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001642031505 none COc1cccc(c2c(C)[nH]nc2NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 19, 32, 32, 32, 19, 19, 19, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 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, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/981 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2c(C)[nH]nc2NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001642031505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642031505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001642031505 none COc1cccc(c2c(C)[nH]nc2NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 19, 32, 32, 32, 19, 19, 19, 4, 4, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 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, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642031505 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 Building ZINC001642031505 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642031505 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 980) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1cccc(c2c(C)[nH]nc2NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001642031505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642031505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001642031505 none COc1cccc(c2c(C)[nH]nc2NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 19, 32, 32, 32, 19, 19, 19, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 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, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 981) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1cccc(c2c(C)[nH]nc2NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001642031505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642031505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001642031505 none COc1cccc(c2c(C)[nH]nc2NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 19, 32, 32, 32, 19, 19, 19, 4, 4, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 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, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642031505 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642031505 Building ZINC001642393502 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642393502 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/982 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3cccc(OCc4ccccc4)c3)CC2)cc1) `ZINC001642393502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642393502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001642393502 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3cccc(OCc4ccccc4)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 14, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 5, 5, 5, 5, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 7, 2, 35, 4, 58, 59, 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, 56, 57]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/983 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3cccc(OCc4ccccc4)c3)CC2)cc1) `ZINC001642393502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642393502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001642393502 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3cccc(OCc4ccccc4)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 15, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 7, 7, 7, 7, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 7, 2, 35, 4, 58, 59, 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, 56, 57]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642393502 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 Building ZINC001642393502 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642393502 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 982) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3cccc(OCc4ccccc4)c3)CC2)cc1) `ZINC001642393502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642393502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001642393502 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3cccc(OCc4ccccc4)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 14, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 5, 5, 5, 5, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 7, 2, 35, 4, 58, 59, 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, 56, 57]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 983) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3cccc(OCc4ccccc4)c3)CC2)cc1) `ZINC001642393502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642393502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001642393502 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3cccc(OCc4ccccc4)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 15, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 7, 7, 7, 7, 1, 1] 50 rigid atoms, others: [0, 1, 34, 3, 32, 5, 6, 33, 7, 2, 35, 4, 58, 59, 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, 56, 57]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642393502 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642393502 Building ZINC001642418527 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642418527 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/984 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C1) `ZINC001642418527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642418527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001642418527 none CC(C)(C)OC(=O)N1CCOc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 19, 19, 19, 19, 19, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 19, 19, 19, 19, 19, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/985 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C1) `ZINC001642418527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642418527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001642418527 none CC(C)(C)OC(=O)N1CCOc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 19, 19, 19, 19, 19, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 19, 19, 19, 19, 19, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642418527 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 Building ZINC001642418527 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642418527 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 984) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)N1CCOc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C1) `ZINC001642418527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642418527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001642418527 none CC(C)(C)OC(=O)N1CCOc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 19, 19, 19, 19, 19, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 19, 19, 19, 19, 19, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 985) grep: /scratch/xiaobo/369383/xbb-8058088.28/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)N1CCOc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C1) `ZINC001642418527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642418527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001642418527 none CC(C)(C)OC(=O)N1CCOc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 26, 19, 19, 19, 19, 19, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 19, 19, 19, 19, 19, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642418527 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418527 Building ZINC001642418889 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642418889 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/986 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCCN(C(=O)OC(C)(C)C)C2) `ZINC001642418889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642418889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001642418889 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCCN(C(=O)OC(C)(C)C)C2 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.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 29, 29, 29, 15, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 29, 2, 2, 2, 2, 2, 2, 3, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29] 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: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/987 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCCN(C(=O)OC(C)(C)C)C2) `ZINC001642418889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642418889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001642418889 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCCN(C(=O)OC(C)(C)C)C2 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.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 29, 29, 29, 15, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 29, 2, 2, 2, 2, 2, 2, 3, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29] 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: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642418889 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 Building ZINC001642418889 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642418889 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 986) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCCN(C(=O)OC(C)(C)C)C2) `ZINC001642418889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642418889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001642418889 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCCN(C(=O)OC(C)(C)C)C2 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.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 29, 29, 29, 15, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 29, 2, 2, 2, 2, 2, 2, 3, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29] 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: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 987) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCCN(C(=O)OC(C)(C)C)C2) `ZINC001642418889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642418889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001642418889 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCCN(C(=O)OC(C)(C)C)C2 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.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 29, 29, 29, 15, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 29, 2, 2, 2, 2, 2, 2, 3, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29] 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: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642418889 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642418889 Building ZINC001642525061 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642525061 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/988 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)Cc2c(cnn2c2ccccc2F)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001642525061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642525061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001642525061 none CC1(C)Cc2c(cnn2c2ccccc2F)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 12, 1, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2, 20, 20] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/989 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)Cc2c(cnn2c2ccccc2F)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001642525061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642525061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001642525061 none CC1(C)Cc2c(cnn2c2ccccc2F)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 12, 1, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 2, 2, 2, 2, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642525061 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 Building ZINC001642525061 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642525061 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 988) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC1(C)Cc2c(cnn2c2ccccc2F)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001642525061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642525061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001642525061 none CC1(C)Cc2c(cnn2c2ccccc2F)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 12, 1, 16, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 2, 2, 2, 2, 20, 20] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 989) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC1(C)Cc2c(cnn2c2ccccc2F)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001642525061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642525061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001642525061 none CC1(C)Cc2c(cnn2c2ccccc2F)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 12, 1, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 2, 2, 2, 2, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642525061 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642525061 Building ZINC001642683835 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642683835 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/990 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC001642683835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642683835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001642683835 none CC(C)(C)OC(=O)N1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 21, 20, 20, 9, 20, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 20, 20, 20, 20, 20, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 9, 9, 8, 8, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/991 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC001642683835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642683835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001642683835 none CC(C)(C)OC(=O)N1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 18, 9, 18, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 9, 9, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642683835 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 Building ZINC001642683835 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642683835 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 990) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC001642683835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642683835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001642683835 none CC(C)(C)OC(=O)N1C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 21, 20, 20, 9, 20, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 20, 20, 20, 20, 20, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 9, 9, 8, 8, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 991) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC001642683835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642683835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001642683835 none CC(C)(C)OC(=O)N1C[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 18, 18, 18, 9, 18, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 9, 9, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642683835 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683835 Building ZINC001642683837 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642683837 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/992 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC001642683837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642683837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001642683837 none CC(C)(C)OC(=O)N1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 19, 18, 18, 10, 18, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 18, 18, 10, 10, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/993 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC001642683837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642683837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001642683837 none CC(C)(C)OC(=O)N1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 21, 19, 21, 19, 19, 9, 19, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 19, 19, 19, 19, 19, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 19, 19, 9, 9, 8, 8, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642683837 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 Building ZINC001642683837 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642683837 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 992) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC001642683837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642683837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001642683837 none CC(C)(C)OC(=O)N1C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 19, 18, 18, 10, 18, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 18, 18, 10, 10, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 993) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: CC(C)(C)OC(=O)N1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21) `ZINC001642683837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642683837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001642683837 none CC(C)(C)OC(=O)N1C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 21, 19, 21, 19, 19, 9, 19, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 19, 19, 19, 19, 19, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 19, 19, 9, 9, 8, 8, 3, 4, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642683837 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642683837 Building ZINC001642792723 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642792723 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/994 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001642792723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642792723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001642792723 none COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3CN2C(=O)OC(C)(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.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.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 28, 28, 28, 28, 6, 6, 6, 13, 13, 13, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/995 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001642792723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642792723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001642792723 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3CN2C(=O)OC(C)(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.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.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 27, 28, 28, 28, 6, 6, 6, 12, 12, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642792723 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 Building ZINC001642792723 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001642792723 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 994) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001642792723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001642792723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001642792723 none COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3CN2C(=O)OC(C)(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.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.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 28, 28, 28, 28, 6, 6, 6, 13, 13, 13, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 995) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3CN2C(=O)OC(C)(C)C)cc1Cl) `ZINC001642792723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001642792723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001642792723 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3CN2C(=O)OC(C)(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.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.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 27, 28, 28, 28, 6, 6, 6, 12, 12, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001642792723 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001642792723 Building ZINC001643249131 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643249131 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/996 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001643249131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643249131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001643249131 none Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 7] 0 hydrogens 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, 3, 9, 9, 18, 26, 35, 35, 35, 35, 35, 35, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 18, 18, 26, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 3, 4, 4, 4, 4, 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, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/997 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001643249131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643249131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001643249131 none Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 7] 0 hydrogens 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, 3, 9, 9, 19, 28, 36, 36, 36, 36, 36, 36, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 5, 19, 19, 28, 36, 36, 36, 36, 36, 36, 36, 36, 36, 9, 3, 4, 4, 4, 4, 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, 51, 52, 53, 54]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001643249131 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 Building ZINC001643249131 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643249131 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 996) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001643249131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643249131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001643249131 none Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 7] 0 hydrogens 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, 3, 9, 9, 18, 26, 35, 35, 35, 35, 35, 35, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 18, 18, 26, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 3, 4, 4, 4, 4, 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, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 997) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001643249131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643249131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001643249131 none Cc1cc(CNC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 7] 0 hydrogens 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, 3, 9, 9, 19, 28, 36, 36, 36, 36, 36, 36, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 5, 19, 19, 28, 36, 36, 36, 36, 36, 36, 36, 36, 36, 9, 3, 4, 4, 4, 4, 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, 51, 52, 53, 54]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001643249131 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643249131 Building ZINC001643276387 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643276387 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/998 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1Oc1cccc(I)c1) `ZINC001643276387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643276387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001643276387 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1Oc1cccc(I)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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', '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, 1, 1, 12, 1, 1, 1, 1, 1, 18, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 5, 5, 19, 50, 50, 33, 50, 50, 50, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 50, 50, 49, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/999 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccccc1Oc1cccc(I)c1) `ZINC001643276387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643276387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001643276387 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccccc1Oc1cccc(I)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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', '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, 1, 1, 12, 1, 1, 1, 1, 1, 18, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 5, 6, 6, 6, 20, 50, 50, 33, 50, 50, 50, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 50, 50, 33, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001643276387 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 Building ZINC001643276387 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001643276387 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 998) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1Oc1cccc(I)c1) `ZINC001643276387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643276387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001643276387 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1Oc1cccc(I)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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', '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, 1, 1, 12, 1, 1, 1, 1, 1, 18, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 5, 5, 19, 50, 50, 33, 50, 50, 50, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 50, 50, 49, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 mkdir: created directory `1' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/1 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 1 (index: 999) grep: /scratch/xiaobo/369383/xbb-8058088.28/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccccc1Oc1cccc(I)c1) `ZINC001643276387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001643276387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001643276387 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccccc1Oc1cccc(I)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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', '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, 1, 1, 12, 1, 1, 1, 1, 1, 18, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 5, 6, 6, 6, 20, 50, 50, 33, 50, 50, 50, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 50, 50, 33, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001643276387 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 1: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/1.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643276387 Building ZINC001643285895 mkdir: created directory `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643285895' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643285895 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001643285895 mkdir: created directory `0' /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643285895/0 /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643285895 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/369383/xbb-8058088.28/working/3D/1000 `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC12CCC(CC1)N2C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001643285895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001643285895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643285895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001643285895 none CC(C)(C)OC(=O)NCC12CCC(CC1)N2C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 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, 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] 0 hydrogens 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, 36, 26, 36, 13, 4, 4, 4, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 26, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643285895 /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Finished preparing ZINC001643285895 Recording results /scratch/xiaobo/369383/xbb-8058088.28/working /scratch/xiaobo/369383/xbb-8058088.28 Appending to /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.* 0: /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643285895/0.* Removing working files in /scratch/xiaobo/369383/xbb-8058088.28/working/building/ZINC001643285895 /scratch/xiaobo/369383/xbb-8058088.28 Compressing combined databse files /scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/369383/xbb-8058088.28/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/369383/xbb-8058088.28/working/3D/1001' removed directory: `/scratch/xiaobo/369383/xbb-8058088.28/working/3D' rmdir: removing directory, `/scratch/xiaobo/369383/xbb-8058088.28/working/building' rmdir: removing directory, `/scratch/xiaobo/369383/xbb-8058088.28/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/369383/xbb-8058088.28' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbb' `/scratch/xiaobo/369383/xbb-8058088.28/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbb/finished' `/scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbb/finished/xbb.db2.gz' removed `/scratch/xiaobo/369383/xbb-8058088.28/finished/xbb.db2.gz' removed directory: `/scratch/xiaobo/369383/xbb-8058088.28/finished' removed directory: `/scratch/xiaobo/369383/xbb-8058088.28'